Starting phenix.real_space_refine on Thu Sep 26 23:37:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lys_23600/09_2024/7lys_23600.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lys_23600/09_2024/7lys_23600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lys_23600/09_2024/7lys_23600.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lys_23600/09_2024/7lys_23600.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lys_23600/09_2024/7lys_23600.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lys_23600/09_2024/7lys_23600.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.171 sd= 1.109 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 899 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: 6 Type Number sf(0) Gaussians P 88 5.49 5 S 14 5.16 5 C 4232 2.51 5 N 1313 2.21 5 O 1552 1.98 5 H 6374 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13573 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 10734 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 39, 'TRANS': 629} Chain breaks: 2 Chain: "B" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 1323 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 35} Chain: "C" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 948 Classifications: {'DNA': 30} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 568 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Time building chain proxies: 7.27, per 1000 atoms: 0.54 Number of scatterers: 13573 At special positions: 0 Unit cell: (84.74, 99.235, 125.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 88 15.00 O 1552 8.00 N 1313 7.00 C 4232 6.00 H 6374 1.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 926.6 milliseconds 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1266 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 48.7% alpha, 9.4% beta 31 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 6.43 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 24 through 39 Processing helix chain 'A' and resid 40 through 48 removed outlier: 4.311A pdb=" N VAL A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 93 through 99 Processing helix chain 'A' and resid 105 through 117 Processing helix chain 'A' and resid 125 through 169 removed outlier: 3.648A pdb=" N LEU A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.740A pdb=" N ARG A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 373 through 384 removed outlier: 4.194A pdb=" N ALA A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 453 removed outlier: 3.838A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 483 removed outlier: 5.461A pdb=" N LYS A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 549 through 566 Processing helix chain 'A' and resid 568 through 597 removed outlier: 3.531A pdb=" N LYS A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 636 through 651 removed outlier: 4.347A pdb=" N THR A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 708 Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 199 removed outlier: 5.741A pdb=" N VAL A 66 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASP A 312 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 262 Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 371 removed outlier: 6.313A pdb=" N LEU A 370 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 391 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A 606 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU A 395 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 388 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG A 407 " --> pdb=" O PRO A 419 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA5, first strand: chain 'A' and resid 516 through 517 removed outlier: 3.562A pdb=" N VAL A 533 " --> pdb=" O PHE A 517 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 5.34 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6365 1.03 - 1.23: 51 1.23 - 1.42: 3348 1.42 - 1.62: 4126 1.62 - 1.81: 19 Bond restraints: 13909 Sorted by residual: bond pdb=" C3' DC D -9 " pdb=" O3' DC D -9 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.55e+00 bond pdb=" C3' DG D -8 " pdb=" O3' DG D -8 " ideal model delta sigma weight residual 1.422 1.451 -0.029 3.00e-02 1.11e+03 9.41e-01 bond pdb=" O4' DC C 3 " pdb=" C1' DC C 3 " ideal model delta sigma weight residual 1.414 1.399 0.015 2.00e-02 2.50e+03 5.65e-01 bond pdb=" O4' DT D -5 " pdb=" C1' DT D -5 " ideal model delta sigma weight residual 1.414 1.399 0.015 2.00e-02 2.50e+03 5.57e-01 bond pdb=" CB ARG A 488 " pdb=" CG ARG A 488 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.15e-01 ... (remaining 13904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 21788 0.83 - 1.66: 2786 1.66 - 2.48: 432 2.48 - 3.31: 127 3.31 - 4.14: 14 Bond angle restraints: 25147 Sorted by residual: angle pdb=" C3' DG D -8 " pdb=" C2' DG D -8 " pdb=" C1' DG D -8 " ideal model delta sigma weight residual 101.60 105.07 -3.47 1.50e+00 4.44e-01 5.35e+00 angle pdb=" C3' DC D 5 " pdb=" C2' DC D 5 " pdb=" C1' DC D 5 " ideal model delta sigma weight residual 101.60 104.72 -3.12 1.50e+00 4.44e-01 4.33e+00 angle pdb=" C4' DC D -9 " pdb=" C3' DC D -9 " pdb=" O3' DC D -9 " ideal model delta sigma weight residual 110.00 113.04 -3.04 1.50e+00 4.44e-01 4.11e+00 angle pdb=" C4' DG D -8 " pdb=" C3' DG D -8 " pdb=" C2' DG D -8 " ideal model delta sigma weight residual 102.40 105.03 -2.63 1.50e+00 4.44e-01 3.08e+00 angle pdb=" C3' DT C -8 " pdb=" C2' DT C -8 " pdb=" C1' DT C -8 " ideal model delta sigma weight residual 101.60 104.10 -2.50 1.50e+00 4.44e-01 2.79e+00 ... (remaining 25142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.78: 5952 33.78 - 67.57: 436 67.57 - 101.35: 20 101.35 - 135.13: 0 135.13 - 168.92: 2 Dihedral angle restraints: 6410 sinusoidal: 4152 harmonic: 2258 Sorted by residual: dihedral pdb=" CA PRO A 171 " pdb=" C PRO A 171 " pdb=" N GLU A 172 " pdb=" CA GLU A 172 " ideal model delta harmonic sigma weight residual -180.00 -159.35 -20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA VAL A 236 " pdb=" C VAL A 236 " pdb=" N VAL A 237 " pdb=" CA VAL A 237 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA PHE A 653 " pdb=" C PHE A 653 " pdb=" N TYR A 654 " pdb=" CA TYR A 654 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 6407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 779 0.029 - 0.058: 297 0.058 - 0.087: 62 0.087 - 0.117: 61 0.117 - 0.146: 8 Chirality restraints: 1207 Sorted by residual: chirality pdb=" CA ILE A 262 " pdb=" N ILE A 262 " pdb=" C ILE A 262 " pdb=" CB ILE A 262 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE A 330 " pdb=" N ILE A 330 " pdb=" C ILE A 330 " pdb=" CB ILE A 330 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA VAL A 302 " pdb=" N VAL A 302 " pdb=" C VAL A 302 " pdb=" CB VAL A 302 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1204 not shown) Planarity restraints: 1746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 620 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 621 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 60 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.09e-01 pdb=" N PRO A 61 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 614 " 0.007 2.00e-02 2.50e+03 6.11e-03 8.39e-01 pdb=" CG HIS A 614 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS A 614 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS A 614 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS A 614 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS A 614 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 HIS A 614 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 HIS A 614 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS A 614 " -0.001 2.00e-02 2.50e+03 ... (remaining 1743 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 815 2.20 - 2.80: 25702 2.80 - 3.40: 35520 3.40 - 4.00: 47770 4.00 - 4.60: 71518 Nonbonded interactions: 181325 Sorted by model distance: nonbonded pdb=" OD1 ASN A 183 " pdb=" H GLU A 184 " model vdw 1.596 2.450 nonbonded pdb=" OE1 GLN A 386 " pdb=" H GLN A 386 " model vdw 1.625 2.450 nonbonded pdb="HH12 ARG A 582 " pdb=" OP2 G B 2 " model vdw 1.626 2.450 nonbonded pdb=" HZ1 LYS A 536 " pdb=" O5' DG C -18 " model vdw 1.636 2.450 nonbonded pdb=" HH TYR A 123 " pdb=" OH TYR A 201 " model vdw 1.679 2.450 ... (remaining 181320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.220 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 37.360 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 0.039 7535 Z= 0.210 Angle : 0.540 4.141 10601 Z= 0.315 Chirality : 0.038 0.146 1207 Planarity : 0.003 0.032 1048 Dihedral : 20.021 168.916 3244 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.17 % Allowed : 5.93 % Favored : 93.89 % 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: -1.46 (0.30), residues: 663 helix: -0.22 (0.29), residues: 295 sheet: -1.50 (0.55), residues: 74 loop : -1.52 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 PHE 0.015 0.001 PHE A 613 TYR 0.010 0.001 TYR A 201 ARG 0.004 0.001 ARG A 538 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 ILE cc_start: 0.9280 (mm) cc_final: 0.9040 (mt) REVERT: A 659 ARG cc_start: 0.8510 (mtt-85) cc_final: 0.8245 (mtt-85) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.5137 time to fit residues: 60.6181 Evaluate side-chains 76 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7535 Z= 0.201 Angle : 0.565 3.864 10601 Z= 0.319 Chirality : 0.039 0.150 1207 Planarity : 0.004 0.036 1048 Dihedral : 21.683 168.852 1908 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.17 % Allowed : 9.60 % Favored : 90.23 % 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: -0.34 (0.32), residues: 663 helix: 0.82 (0.30), residues: 303 sheet: -1.33 (0.58), residues: 74 loop : -1.00 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 PHE 0.018 0.001 PHE A 613 TYR 0.008 0.001 TYR A 654 ARG 0.004 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8370 (ttm170) cc_final: 0.7978 (mtt-85) REVERT: A 659 ARG cc_start: 0.8214 (mtt-85) cc_final: 0.7970 (mtt-85) outliers start: 1 outliers final: 1 residues processed: 80 average time/residue: 0.6295 time to fit residues: 61.6778 Evaluate side-chains 70 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.0370 chunk 18 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7535 Z= 0.233 Angle : 0.549 4.596 10601 Z= 0.308 Chirality : 0.039 0.140 1207 Planarity : 0.005 0.059 1048 Dihedral : 21.635 170.836 1908 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.70 % Allowed : 10.47 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.33), residues: 663 helix: 1.38 (0.31), residues: 305 sheet: -1.68 (0.56), residues: 79 loop : -0.81 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 308 HIS 0.007 0.002 HIS A 614 PHE 0.015 0.001 PHE A 613 TYR 0.009 0.001 TYR A 654 ARG 0.007 0.000 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8417 (ttm170) cc_final: 0.8084 (mtt-85) REVERT: A 659 ARG cc_start: 0.8246 (mtt-85) cc_final: 0.7994 (mtt-85) outliers start: 4 outliers final: 4 residues processed: 78 average time/residue: 0.6035 time to fit residues: 57.9718 Evaluate side-chains 75 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 chunk 45 optimal weight: 0.0970 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7535 Z= 0.144 Angle : 0.512 4.886 10601 Z= 0.286 Chirality : 0.037 0.141 1207 Planarity : 0.004 0.037 1048 Dihedral : 21.549 170.501 1908 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.52 % Allowed : 12.39 % Favored : 87.09 % 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: 0.52 (0.34), residues: 663 helix: 1.66 (0.31), residues: 306 sheet: -1.45 (0.56), residues: 74 loop : -0.56 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 PHE 0.016 0.001 PHE A 354 TYR 0.010 0.001 TYR A 654 ARG 0.006 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8326 (tp) REVERT: A 284 ARG cc_start: 0.8373 (ttm170) cc_final: 0.8017 (mtt-85) REVERT: A 659 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.7978 (mtt-85) outliers start: 3 outliers final: 2 residues processed: 78 average time/residue: 0.5973 time to fit residues: 57.0831 Evaluate side-chains 73 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 325 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7535 Z= 0.314 Angle : 0.564 5.043 10601 Z= 0.315 Chirality : 0.041 0.144 1207 Planarity : 0.004 0.035 1048 Dihedral : 21.541 169.588 1908 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.05 % Allowed : 13.61 % Favored : 85.34 % 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: 0.39 (0.34), residues: 663 helix: 1.66 (0.31), residues: 306 sheet: -1.76 (0.55), residues: 74 loop : -0.68 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 308 HIS 0.007 0.002 HIS A 614 PHE 0.016 0.001 PHE A 613 TYR 0.010 0.001 TYR A 654 ARG 0.004 0.000 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8318 (tp) REVERT: A 79 MET cc_start: 0.8377 (mmm) cc_final: 0.8164 (mmm) REVERT: A 284 ARG cc_start: 0.8451 (ttm170) cc_final: 0.8088 (mtt-85) outliers start: 6 outliers final: 5 residues processed: 76 average time/residue: 0.6156 time to fit residues: 57.4888 Evaluate side-chains 72 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.0970 chunk 64 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7535 Z= 0.160 Angle : 0.512 4.102 10601 Z= 0.286 Chirality : 0.038 0.140 1207 Planarity : 0.004 0.053 1048 Dihedral : 21.504 170.024 1908 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.70 % Allowed : 13.61 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.34), residues: 663 helix: 1.88 (0.31), residues: 306 sheet: -1.67 (0.55), residues: 74 loop : -0.56 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 308 HIS 0.006 0.001 HIS A 614 PHE 0.015 0.001 PHE A 354 TYR 0.010 0.001 TYR A 654 ARG 0.005 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8301 (tp) REVERT: A 284 ARG cc_start: 0.8395 (ttm170) cc_final: 0.8024 (mtt-85) outliers start: 4 outliers final: 2 residues processed: 77 average time/residue: 0.5722 time to fit residues: 54.6462 Evaluate side-chains 72 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 325 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7535 Z= 0.280 Angle : 0.547 4.127 10601 Z= 0.306 Chirality : 0.041 0.137 1207 Planarity : 0.004 0.035 1048 Dihedral : 21.489 169.454 1908 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.87 % Allowed : 13.79 % Favored : 85.34 % 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: 0.58 (0.34), residues: 663 helix: 1.84 (0.31), residues: 305 sheet: -1.78 (0.54), residues: 74 loop : -0.57 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 308 HIS 0.007 0.001 HIS A 614 PHE 0.014 0.001 PHE A 354 TYR 0.010 0.001 TYR A 654 ARG 0.006 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 71 average time/residue: 0.5679 time to fit residues: 50.7080 Evaluate side-chains 72 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 0.0670 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7535 Z= 0.162 Angle : 0.515 4.177 10601 Z= 0.287 Chirality : 0.038 0.137 1207 Planarity : 0.004 0.054 1048 Dihedral : 21.458 169.620 1908 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.87 % Allowed : 13.79 % Favored : 85.34 % 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: 0.77 (0.34), residues: 663 helix: 1.97 (0.31), residues: 306 sheet: -1.43 (0.57), residues: 64 loop : -0.58 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 308 HIS 0.006 0.001 HIS A 614 PHE 0.012 0.001 PHE A 354 TYR 0.010 0.001 TYR A 654 ARG 0.007 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.8022 (mtt-85) REVERT: A 606 GLU cc_start: 0.8203 (tt0) cc_final: 0.7923 (tt0) outliers start: 5 outliers final: 5 residues processed: 76 average time/residue: 0.5412 time to fit residues: 52.0394 Evaluate side-chains 75 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7535 Z= 0.162 Angle : 0.507 4.287 10601 Z= 0.284 Chirality : 0.037 0.135 1207 Planarity : 0.004 0.048 1048 Dihedral : 21.397 169.449 1908 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.70 % Allowed : 14.31 % Favored : 84.99 % 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 (0.34), residues: 663 helix: 2.03 (0.31), residues: 305 sheet: -1.38 (0.57), residues: 64 loop : -0.53 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 308 HIS 0.005 0.001 HIS A 614 PHE 0.013 0.001 PHE A 354 TYR 0.010 0.001 TYR A 654 ARG 0.008 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8315 (mtm-85) cc_final: 0.8030 (mtt-85) outliers start: 4 outliers final: 4 residues processed: 76 average time/residue: 0.5656 time to fit residues: 53.8008 Evaluate side-chains 76 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.0030 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7535 Z= 0.223 Angle : 0.527 4.330 10601 Z= 0.294 Chirality : 0.039 0.135 1207 Planarity : 0.005 0.060 1048 Dihedral : 21.399 168.785 1908 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.05 % Allowed : 13.96 % Favored : 84.99 % 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 (0.34), residues: 663 helix: 2.04 (0.31), residues: 304 sheet: -1.35 (0.56), residues: 64 loop : -0.56 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 308 HIS 0.006 0.001 HIS A 614 PHE 0.013 0.001 PHE A 613 TYR 0.009 0.001 TYR A 654 ARG 0.008 0.000 ARG A 575 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1326 Ramachandran restraints generated. 663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ARG cc_start: 0.8350 (mtm-85) cc_final: 0.8068 (mtt-85) REVERT: A 487 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8345 (mtmm) outliers start: 6 outliers final: 6 residues processed: 73 average time/residue: 0.5870 time to fit residues: 53.5245 Evaluate side-chains 76 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 0.0870 chunk 3 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.077761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.068108 restraints weight = 42837.062| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.64 r_work: 0.2872 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7535 Z= 0.172 Angle : 0.512 4.376 10601 Z= 0.286 Chirality : 0.038 0.137 1207 Planarity : 0.004 0.055 1048 Dihedral : 21.381 168.942 1908 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.87 % Allowed : 14.14 % Favored : 84.99 % 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: 0.93 (0.34), residues: 663 helix: 2.12 (0.31), residues: 304 sheet: -1.23 (0.57), residues: 64 loop : -0.53 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 308 HIS 0.006 0.001 HIS A 614 PHE 0.013 0.001 PHE A 354 TYR 0.010 0.001 TYR A 654 ARG 0.008 0.000 ARG A 575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3811.19 seconds wall clock time: 66 minutes 54.53 seconds (4014.53 seconds total)