Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 04:34:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoj_33983/04_2023/7yoj_33983.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoj_33983/04_2023/7yoj_33983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoj_33983/04_2023/7yoj_33983.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoj_33983/04_2023/7yoj_33983.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoj_33983/04_2023/7yoj_33983.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yoj_33983/04_2023/7yoj_33983.pdb" } resolution = 3.36 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= 0.005 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 216 5.49 5 S 24 5.16 5 C 6436 2.51 5 N 2166 2.21 5 O 2703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A ASP 71": "OD1" <-> "OD2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A ASP 219": "OD1" <-> "OD2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 472": "OD1" <-> "OD2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11545 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6947 Classifications: {'peptide': 867} Link IDs: {'PTRANS': 50, 'TRANS': 816} Chain: "C" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 248 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 612 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "B" Number of atoms: 3738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 3738 Classifications: {'RNA': 174} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 10, 'rna3p_pur': 90, 'rna3p_pyr': 64} Link IDs: {'rna2p': 20, 'rna3p': 153} Time building chain proxies: 6.77, per 1000 atoms: 0.59 Number of scatterers: 11545 At special positions: 0 Unit cell: (107.856, 110.424, 128.4, 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 24 16.00 P 216 15.00 O 2703 8.00 N 2166 7.00 C 6436 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: 6.86 Conformation dependent library (CDL) restraints added in 1.1 seconds 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1622 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 43.8% alpha, 9.1% beta 72 base pairs and 127 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 1 through 40 Processing helix chain 'A' and resid 48 through 70 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 170 through 183 removed outlier: 3.615A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 197 Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.822A pdb=" N TRP A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 removed outlier: 3.626A pdb=" N LEU A 224 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 220 through 225' Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 234 through 260 removed outlier: 3.548A pdb=" N THR A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 287 Processing helix chain 'A' and resid 320 through 334 removed outlier: 3.817A pdb=" N VAL A 324 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 removed outlier: 4.183A pdb=" N PHE A 340 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 366 Processing helix chain 'A' and resid 431 through 436 removed outlier: 4.524A pdb=" N ASP A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 431 through 436' Processing helix chain 'A' and resid 441 through 445 removed outlier: 3.561A pdb=" N GLY A 444 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 445' Processing helix chain 'A' and resid 457 through 468 Processing helix chain 'A' and resid 565 through 589 removed outlier: 3.575A pdb=" N ASN A 588 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 612 Processing helix chain 'A' and resid 615 through 633 Processing helix chain 'A' and resid 659 through 674 removed outlier: 3.771A pdb=" N LYS A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.571A pdb=" N VAL A 698 " --> pdb=" O THR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 717 Processing helix chain 'A' and resid 795 through 814 Proline residue: A 807 - end of helix Processing helix chain 'A' and resid 818 through 830 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 861 through 866 Processing sheet with id=AA1, first strand: chain 'A' and resid 383 through 385 removed outlier: 3.531A pdb=" N ARG A 502 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU A 503 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU A 147 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 450 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET A 452 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 454 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU A 407 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 292 Processing sheet with id=AA3, first strand: chain 'A' and resid 481 through 486 removed outlier: 5.289A pdb=" N HIS A 483 " --> pdb=" O LYS A 510 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS A 510 " --> pdb=" O HIS A 483 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 485 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 687 through 690 removed outlier: 7.608A pdb=" N VAL A 641 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE A 534 " --> pdb=" O VAL A 641 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ALA A 643 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE A 536 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 535 " --> pdb=" O ALA A 547 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A 548 " --> pdb=" O ILE A 557 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 739 through 740 removed outlier: 3.573A pdb=" N GLY A 854 " --> pdb=" O VAL A 845 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 858 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 841 " --> pdb=" O ILE A 858 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 792 " --> pdb=" O TYR A 842 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 781 through 782 302 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 192 hydrogen bonds 372 hydrogen bond angles 0 basepair planarities 72 basepair parallelities 127 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 6.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1520 1.32 - 1.45: 4485 1.45 - 1.57: 5779 1.57 - 1.69: 429 1.69 - 1.82: 35 Bond restraints: 12248 Sorted by residual: bond pdb=" C PRO A 114 " pdb=" O PRO A 114 " ideal model delta sigma weight residual 1.240 1.197 0.044 1.12e-02 7.97e+03 1.53e+01 bond pdb=" N ASP A 219 " pdb=" CA ASP A 219 " ideal model delta sigma weight residual 1.457 1.491 -0.035 1.33e-02 5.65e+03 6.75e+00 bond pdb=" N ARG A 107 " pdb=" CA ARG A 107 " ideal model delta sigma weight residual 1.464 1.489 -0.025 9.80e-03 1.04e+04 6.64e+00 bond pdb=" N ILE A 113 " pdb=" CA ILE A 113 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.23e-02 6.61e+03 6.61e+00 bond pdb=" N VAL A 473 " pdb=" CA VAL A 473 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.17e-02 7.31e+03 6.57e+00 ... (remaining 12243 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.22: 1444 106.22 - 113.22: 6671 113.22 - 120.22: 4753 120.22 - 127.22: 4139 127.22 - 134.22: 583 Bond angle restraints: 17590 Sorted by residual: angle pdb=" O3' G B 155 " pdb=" C3' G B 155 " pdb=" C2' G B 155 " ideal model delta sigma weight residual 109.50 119.83 -10.33 1.50e+00 4.44e-01 4.74e+01 angle pdb=" CA PRO A 862 " pdb=" N PRO A 862 " pdb=" CD PRO A 862 " ideal model delta sigma weight residual 112.00 105.22 6.78 1.40e+00 5.10e-01 2.35e+01 angle pdb=" N VAL A 88 " pdb=" CA VAL A 88 " pdb=" C VAL A 88 " ideal model delta sigma weight residual 108.88 118.11 -9.23 2.16e+00 2.14e-01 1.83e+01 angle pdb=" N LEU A 331 " pdb=" CA LEU A 331 " pdb=" C LEU A 331 " ideal model delta sigma weight residual 111.36 107.06 4.30 1.09e+00 8.42e-01 1.55e+01 angle pdb=" N LEU A 38 " pdb=" CA LEU A 38 " pdb=" C LEU A 38 " ideal model delta sigma weight residual 111.71 107.19 4.52 1.15e+00 7.56e-01 1.55e+01 ... (remaining 17585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.61: 6319 34.61 - 69.23: 496 69.23 - 103.84: 44 103.84 - 138.45: 4 138.45 - 173.07: 4 Dihedral angle restraints: 6867 sinusoidal: 4358 harmonic: 2509 Sorted by residual: dihedral pdb=" O4' U B 26 " pdb=" C1' U B 26 " pdb=" N1 U B 26 " pdb=" C2 U B 26 " ideal model delta sinusoidal sigma weight residual -160.00 -0.88 -159.12 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' U B 148 " pdb=" C1' U B 148 " pdb=" N1 U B 148 " pdb=" C2 U B 148 " ideal model delta sinusoidal sigma weight residual -160.00 -18.27 -141.73 1 1.50e+01 4.44e-03 7.62e+01 dihedral pdb=" O4' C B 66 " pdb=" C1' C B 66 " pdb=" N1 C B 66 " pdb=" C2 C B 66 " ideal model delta sinusoidal sigma weight residual -160.00 -70.12 -89.88 1 1.50e+01 4.44e-03 4.26e+01 ... (remaining 6864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1865 0.085 - 0.169: 156 0.169 - 0.254: 24 0.254 - 0.338: 2 0.338 - 0.423: 3 Chirality restraints: 2050 Sorted by residual: chirality pdb=" P U B 99 " pdb=" OP1 U B 99 " pdb=" OP2 U B 99 " pdb=" O5' U B 99 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" C3' G B 155 " pdb=" C4' G B 155 " pdb=" O3' G B 155 " pdb=" C2' G B 155 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CG LEU A 50 " pdb=" CB LEU A 50 " pdb=" CD1 LEU A 50 " pdb=" CD2 LEU A 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 2047 not shown) Planarity restraints: 1474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 861 " 0.091 5.00e-02 4.00e+02 1.35e-01 2.90e+01 pdb=" N PRO A 862 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO A 862 " 0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 862 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 71 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" CG ASP A 71 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP A 71 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP A 71 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 143 " 0.038 5.00e-02 4.00e+02 5.69e-02 5.19e+00 pdb=" N PRO A 144 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " 0.032 5.00e-02 4.00e+02 ... (remaining 1471 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3217 2.82 - 3.34: 10218 3.34 - 3.86: 23012 3.86 - 4.38: 25418 4.38 - 4.90: 36931 Nonbonded interactions: 98796 Sorted by model distance: nonbonded pdb=" OH TYR A 730 " pdb=" O ARG A 852 " model vdw 2.304 2.440 nonbonded pdb=" O2' G B 153 " pdb=" OP1 G B 155 " model vdw 2.311 2.440 nonbonded pdb=" OH TYR A 544 " pdb=" OG SER A 621 " model vdw 2.316 2.440 nonbonded pdb=" O SER A 771 " pdb=" OG SER A 771 " model vdw 2.321 2.440 nonbonded pdb=" O SER A 757 " pdb=" OG SER A 757 " model vdw 2.327 2.440 ... (remaining 98791 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.000 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 39.810 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 12248 Z= 0.281 Angle : 0.870 10.333 17590 Z= 0.477 Chirality : 0.053 0.423 2050 Planarity : 0.007 0.135 1474 Dihedral : 20.715 173.068 5245 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.90 % Favored : 93.64 % Rotamer Outliers : 2.19 % 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: -2.03 (0.25), residues: 865 helix: -0.88 (0.24), residues: 336 sheet: -1.83 (0.60), residues: 71 loop : -1.59 (0.27), residues: 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 81 average time/residue: 0.3024 time to fit residues: 33.5884 Evaluate side-chains 65 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2695 time to fit residues: 4.1394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 30.0000 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 12248 Z= 0.239 Angle : 0.633 7.401 17590 Z= 0.321 Chirality : 0.037 0.298 2050 Planarity : 0.005 0.087 1474 Dihedral : 19.036 176.445 3475 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.62 % Favored : 95.26 % Rotamer Outliers : 1.50 % 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: -0.84 (0.28), residues: 865 helix: 0.69 (0.28), residues: 341 sheet: -1.97 (0.48), residues: 96 loop : -1.22 (0.30), residues: 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 1.098 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 68 average time/residue: 0.3014 time to fit residues: 28.4873 Evaluate side-chains 60 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1102 time to fit residues: 2.5754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 670 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 12248 Z= 0.269 Angle : 0.648 9.812 17590 Z= 0.328 Chirality : 0.037 0.261 2050 Planarity : 0.005 0.068 1474 Dihedral : 19.086 174.974 3475 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.43 % Favored : 94.45 % Rotamer Outliers : 2.19 % 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: -0.46 (0.29), residues: 865 helix: 1.14 (0.28), residues: 339 sheet: -1.95 (0.49), residues: 96 loop : -1.08 (0.30), residues: 430 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 77 average time/residue: 0.3058 time to fit residues: 32.8035 Evaluate side-chains 60 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3021 time to fit residues: 3.8668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 103 optimal weight: 40.0000 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 12248 Z= 0.247 Angle : 0.628 11.613 17590 Z= 0.317 Chirality : 0.036 0.257 2050 Planarity : 0.005 0.059 1474 Dihedral : 19.123 174.700 3475 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.32 % Favored : 94.57 % Rotamer Outliers : 3.28 % 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: -0.32 (0.29), residues: 865 helix: 1.29 (0.28), residues: 342 sheet: -1.92 (0.50), residues: 96 loop : -1.04 (0.31), residues: 427 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 60 time to evaluate : 1.066 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 81 average time/residue: 0.2400 time to fit residues: 28.7483 Evaluate side-chains 69 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1030 time to fit residues: 3.8060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN A 308 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN A 670 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 12248 Z= 0.376 Angle : 0.717 11.806 17590 Z= 0.364 Chirality : 0.040 0.334 2050 Planarity : 0.005 0.051 1474 Dihedral : 19.405 179.847 3475 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.17 % Favored : 92.72 % Rotamer Outliers : 2.87 % 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: -0.50 (0.29), residues: 865 helix: 1.22 (0.28), residues: 341 sheet: -2.39 (0.49), residues: 105 loop : -1.05 (0.31), residues: 419 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 62 time to evaluate : 1.093 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 79 average time/residue: 0.2557 time to fit residues: 29.5955 Evaluate side-chains 63 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1117 time to fit residues: 3.5235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.0970 chunk 93 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 40.0000 chunk 85 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 12248 Z= 0.243 Angle : 0.636 8.262 17590 Z= 0.321 Chirality : 0.037 0.262 2050 Planarity : 0.004 0.050 1474 Dihedral : 19.325 174.215 3475 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.55 % Favored : 94.34 % Rotamer Outliers : 1.23 % 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: -0.16 (0.29), residues: 865 helix: 1.49 (0.28), residues: 342 sheet: -1.89 (0.52), residues: 95 loop : -0.99 (0.32), residues: 428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 1.023 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 0.2707 time to fit residues: 26.1658 Evaluate side-chains 60 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1480 time to fit residues: 2.9024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 103 optimal weight: 40.0000 chunk 64 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12248 Z= 0.170 Angle : 0.606 7.905 17590 Z= 0.303 Chirality : 0.035 0.234 2050 Planarity : 0.004 0.041 1474 Dihedral : 19.155 177.070 3475 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.32 % Favored : 94.57 % Rotamer Outliers : 1.09 % 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: 0.04 (0.30), residues: 865 helix: 1.78 (0.28), residues: 340 sheet: -1.80 (0.52), residues: 96 loop : -0.98 (0.31), residues: 429 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 1.097 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 67 average time/residue: 0.2717 time to fit residues: 26.4516 Evaluate side-chains 59 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1115 time to fit residues: 2.1891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 12248 Z= 0.279 Angle : 0.650 8.028 17590 Z= 0.327 Chirality : 0.037 0.255 2050 Planarity : 0.004 0.042 1474 Dihedral : 19.209 173.561 3475 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.01 % Favored : 93.87 % Rotamer Outliers : 1.23 % 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: -0.01 (0.30), residues: 865 helix: 1.73 (0.28), residues: 340 sheet: -1.83 (0.53), residues: 96 loop : -0.99 (0.31), residues: 429 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 1.215 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 61 average time/residue: 0.2646 time to fit residues: 23.7438 Evaluate side-chains 58 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.951 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1202 time to fit residues: 1.8355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 30.0000 chunk 96 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.076 12248 Z= 0.475 Angle : 0.780 10.536 17590 Z= 0.395 Chirality : 0.043 0.338 2050 Planarity : 0.005 0.045 1474 Dihedral : 19.803 172.337 3475 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.40 % Favored : 92.37 % Rotamer Outliers : 0.68 % 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: -0.52 (0.29), residues: 865 helix: 1.29 (0.27), residues: 341 sheet: -2.56 (0.49), residues: 105 loop : -1.10 (0.31), residues: 419 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 1.058 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.2489 time to fit residues: 22.3033 Evaluate side-chains 57 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2567 time to fit residues: 2.5711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 90 optimal weight: 20.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 12248 Z= 0.301 Angle : 0.691 8.563 17590 Z= 0.350 Chirality : 0.039 0.286 2050 Planarity : 0.005 0.048 1474 Dihedral : 19.684 171.342 3475 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.01 % Favored : 93.87 % Rotamer Outliers : 0.55 % 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: -0.36 (0.30), residues: 865 helix: 1.51 (0.28), residues: 336 sheet: -2.47 (0.49), residues: 105 loop : -1.07 (0.32), residues: 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 1.018 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 58 average time/residue: 0.2637 time to fit residues: 22.5987 Evaluate side-chains 54 residues out of total 732 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.919 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1012 time to fit residues: 1.7581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.0370 chunk 78 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 10 optimal weight: 0.0770 chunk 15 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.160329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.116518 restraints weight = 26870.003| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.81 r_work: 0.3519 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 12248 Z= 0.151 Angle : 0.625 13.661 17590 Z= 0.310 Chirality : 0.034 0.207 2050 Planarity : 0.004 0.047 1474 Dihedral : 19.104 179.113 3475 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 0.27 % 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: 0.21 (0.30), residues: 865 helix: 1.98 (0.28), residues: 339 sheet: -1.62 (0.55), residues: 94 loop : -0.97 (0.32), residues: 432 =============================================================================== Job complete usr+sys time: 2046.34 seconds wall clock time: 38 minutes 18.66 seconds (2298.66 seconds total)