Starting phenix.real_space_refine on Mon Mar 11 11:13:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctl_26994/03_2024/8ctl_26994_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctl_26994/03_2024/8ctl_26994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctl_26994/03_2024/8ctl_26994.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctl_26994/03_2024/8ctl_26994.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctl_26994/03_2024/8ctl_26994_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ctl_26994/03_2024/8ctl_26994_neut.pdb" } resolution = 3.1 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= -0.001 sd= 0.028 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 233 5.49 5 S 21 5.16 5 C 4257 2.51 5 N 1486 2.21 5 O 2141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D GLU 84": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D GLU 149": "OE1" <-> "OE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 410": "OE1" <-> "OE2" Residue "D GLU 411": "OE1" <-> "OE2" Residue "D GLU 449": "OE1" <-> "OE2" Residue "D GLU 459": "OE1" <-> "OE2" Residue "D GLU 473": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8138 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3209 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 382} Chain breaks: 1 Chain: "C" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 3937 Classifications: {'RNA': 184} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 11, 'rna3p_pur': 89, 'rna3p_pyr': 69} Link IDs: {'rna2p': 26, 'rna3p': 157} Chain breaks: 2 Chain: "A" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 579 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "B" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Time building chain proxies: 5.34, per 1000 atoms: 0.66 Number of scatterers: 8138 At special positions: 0 Unit cell: (89.88, 103.79, 131.61, 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 21 16.00 P 233 15.00 O 2141 8.00 N 1486 7.00 C 4257 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.85 Conformation dependent library (CDL) restraints added in 940.0 milliseconds 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 6 sheets defined 29.9% alpha, 18.2% beta 75 base pairs and 130 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'D' and resid 20 through 29 removed outlier: 3.755A pdb=" N LEU D 27 " --> pdb=" O VAL D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 108 Processing helix chain 'D' and resid 109 through 121 Processing helix chain 'D' and resid 163 through 181 Processing helix chain 'D' and resid 297 through 313 Proline residue: D 304 - end of helix Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 341 through 349 removed outlier: 3.658A pdb=" N CYS D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 416 Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 480 through 482 No H-bonds generated for 'chain 'D' and resid 480 through 482' Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 14 removed outlier: 4.626A pdb=" N VAL D 6 " --> pdb=" O LEU D 14 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR D 5 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU D 44 " --> pdb=" O TYR D 5 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE D 7 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR D 41 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 318 through 322 removed outlier: 6.256A pdb=" N VAL D 189 " --> pdb=" O CYS D 319 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR D 321 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU D 191 " --> pdb=" O THR D 321 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET D 68 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR D 72 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N SER D 77 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL D 367 " --> pdb=" O GLN D 82 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N MET D 366 " --> pdb=" O TYR D 494 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 128 through 131 Processing sheet with id=AA4, first strand: chain 'D' and resid 378 through 380 Processing sheet with id=AA5, first strand: chain 'D' and resid 387 through 388 removed outlier: 6.045A pdb=" N TYR D 387 " --> pdb=" O VAL D 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 476 through 478 removed outlier: 6.535A pdb=" N TYR D 468 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER D 458 " --> pdb=" O TYR D 468 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL D 470 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL D 446 " --> pdb=" O TYR D 484 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR D 484 " --> pdb=" O VAL D 446 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 190 hydrogen bonds 356 hydrogen bond angles 0 basepair planarities 75 basepair parallelities 130 stacking parallelities Total time for adding SS restraints: 3.43 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 785 1.30 - 1.43: 3479 1.43 - 1.56: 4025 1.56 - 1.69: 460 1.69 - 1.81: 33 Bond restraints: 8782 Sorted by residual: bond pdb=" CA ARG D 131 " pdb=" C ARG D 131 " ideal model delta sigma weight residual 1.526 1.456 0.070 1.20e-02 6.94e+03 3.38e+01 bond pdb=" CA ALA D 381 " pdb=" C ALA D 381 " ideal model delta sigma weight residual 1.526 1.452 0.074 1.30e-02 5.92e+03 3.20e+01 bond pdb=" CA ARG D 371 " pdb=" C ARG D 371 " ideal model delta sigma weight residual 1.525 1.460 0.065 1.28e-02 6.10e+03 2.55e+01 bond pdb=" N GLN D 465 " pdb=" CA GLN D 465 " ideal model delta sigma weight residual 1.461 1.402 0.059 1.20e-02 6.94e+03 2.46e+01 bond pdb=" C ARG D 131 " pdb=" O ARG D 131 " ideal model delta sigma weight residual 1.235 1.178 0.056 1.14e-02 7.69e+03 2.45e+01 ... (remaining 8777 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.66: 1219 105.66 - 112.80: 4967 112.80 - 119.93: 3362 119.93 - 127.07: 2863 127.07 - 134.20: 546 Bond angle restraints: 12957 Sorted by residual: angle pdb=" N THR D 352 " pdb=" CA THR D 352 " pdb=" C THR D 352 " ideal model delta sigma weight residual 111.03 121.20 -10.17 1.11e+00 8.12e-01 8.39e+01 angle pdb=" N ARG D 398 " pdb=" CA ARG D 398 " pdb=" C ARG D 398 " ideal model delta sigma weight residual 113.41 102.54 10.87 1.22e+00 6.72e-01 7.95e+01 angle pdb=" N ILE D 439 " pdb=" CA ILE D 439 " pdb=" C ILE D 439 " ideal model delta sigma weight residual 108.93 99.38 9.55 1.35e+00 5.49e-01 5.00e+01 angle pdb=" CA GLY D 460 " pdb=" C GLY D 460 " pdb=" O GLY D 460 " ideal model delta sigma weight residual 122.22 117.63 4.59 6.50e-01 2.37e+00 4.98e+01 angle pdb=" C THR D 352 " pdb=" CA THR D 352 " pdb=" CB THR D 352 " ideal model delta sigma weight residual 110.95 100.80 10.15 1.55e+00 4.16e-01 4.29e+01 ... (remaining 12952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 4525 35.28 - 70.56: 733 70.56 - 105.84: 69 105.84 - 141.12: 11 141.12 - 176.40: 13 Dihedral angle restraints: 5351 sinusoidal: 4183 harmonic: 1168 Sorted by residual: dihedral pdb=" C5' A C 93 " pdb=" C4' A C 93 " pdb=" C3' A C 93 " pdb=" O3' A C 93 " ideal model delta sinusoidal sigma weight residual 147.00 77.07 69.93 1 8.00e+00 1.56e-02 9.85e+01 dihedral pdb=" O4' C C 60 " pdb=" C1' C C 60 " pdb=" N1 C C 60 " pdb=" C2 C C 60 " ideal model delta sinusoidal sigma weight residual 200.00 31.04 168.96 1 1.50e+01 4.44e-03 8.45e+01 dihedral pdb=" C4' A C 93 " pdb=" C3' A C 93 " pdb=" C2' A C 93 " pdb=" C1' A C 93 " ideal model delta sinusoidal sigma weight residual -35.00 27.93 -62.93 1 8.00e+00 1.56e-02 8.17e+01 ... (remaining 5348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1037 0.081 - 0.163: 443 0.163 - 0.244: 102 0.244 - 0.325: 5 0.325 - 0.406: 5 Chirality restraints: 1592 Sorted by residual: chirality pdb=" CA LYS D 31 " pdb=" N LYS D 31 " pdb=" C LYS D 31 " pdb=" CB LYS D 31 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" C3' DT B 113 " pdb=" C4' DT B 113 " pdb=" O3' DT B 113 " pdb=" C2' DT B 113 " both_signs ideal model delta sigma weight residual False -2.66 -2.27 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA ASN D 382 " pdb=" N ASN D 382 " pdb=" C ASN D 382 " pdb=" CB ASN D 382 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 1589 not shown) Planarity restraints: 798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC A 27 " 0.052 2.00e-02 2.50e+03 2.51e-02 1.42e+01 pdb=" N1 DC A 27 " -0.048 2.00e-02 2.50e+03 pdb=" C2 DC A 27 " -0.008 2.00e-02 2.50e+03 pdb=" O2 DC A 27 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DC A 27 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DC A 27 " 0.012 2.00e-02 2.50e+03 pdb=" N4 DC A 27 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DC A 27 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DC A 27 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 78 " 0.048 2.00e-02 2.50e+03 2.24e-02 1.38e+01 pdb=" N9 A C 78 " -0.053 2.00e-02 2.50e+03 pdb=" C8 A C 78 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A C 78 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A C 78 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A C 78 " 0.009 2.00e-02 2.50e+03 pdb=" N6 A C 78 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A C 78 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A C 78 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A C 78 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A C 78 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG A 9 " 0.038 2.00e-02 2.50e+03 1.94e-02 1.13e+01 pdb=" N9 DG A 9 " -0.051 2.00e-02 2.50e+03 pdb=" C8 DG A 9 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG A 9 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DG A 9 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DG A 9 " 0.013 2.00e-02 2.50e+03 pdb=" O6 DG A 9 " -0.003 2.00e-02 2.50e+03 pdb=" N1 DG A 9 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG A 9 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG A 9 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG A 9 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DG A 9 " -0.008 2.00e-02 2.50e+03 ... (remaining 795 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2129 2.80 - 3.33: 7862 3.33 - 3.85: 17670 3.85 - 4.38: 20559 4.38 - 4.90: 26863 Nonbonded interactions: 75083 Sorted by model distance: nonbonded pdb=" OG SER D 8 " pdb=" OG SER D 10 " model vdw 2.280 2.440 nonbonded pdb=" O2' G C 95 " pdb=" N2 G C 131 " model vdw 2.309 2.520 nonbonded pdb=" OD1 ASN D 154 " pdb=" O2' U C 125 " model vdw 2.321 2.440 nonbonded pdb=" N3 C C 111 " pdb=" O6 G C 172 " model vdw 2.327 2.496 nonbonded pdb=" O ASN D 154 " pdb=" O2' C C 98 " model vdw 2.352 2.440 ... (remaining 75078 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.020 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.260 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4489 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 : 0.009 0.074 8782 Z= 0.596 Angle : 1.320 10.875 12957 Z= 0.934 Chirality : 0.090 0.406 1592 Planarity : 0.005 0.071 798 Dihedral : 27.577 176.404 4599 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 32.18 Ramachandran Plot: Outliers : 0.50 % Allowed : 12.09 % Favored : 87.41 % Rotamer: Outliers : 7.20 % Allowed : 17.00 % Favored : 75.79 % Cbeta Deviations : 1.06 % Peptide Plane: Cis-proline : 5.56 % 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: -5.68 (0.29), residues: 397 helix: -4.32 (0.23), residues: 113 sheet: -3.35 (0.52), residues: 72 loop : -3.66 (0.30), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 161 HIS 0.008 0.002 HIS D 373 PHE 0.012 0.002 PHE D 196 TYR 0.011 0.002 TYR D 433 ARG 0.003 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 175 ASN cc_start: 0.6018 (m-40) cc_final: 0.5698 (m-40) REVERT: D 443 SER cc_start: 0.6737 (m) cc_final: 0.6077 (t) REVERT: D 470 VAL cc_start: 0.5463 (OUTLIER) cc_final: 0.5218 (t) outliers start: 25 outliers final: 3 residues processed: 129 average time/residue: 0.3099 time to fit residues: 48.7437 Evaluate side-chains 77 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 470 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN D 317 ASN ** D 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS D 376 GLN ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 462 ASN D 465 GLN D 487 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5176 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 8782 Z= 0.321 Angle : 0.935 14.274 12957 Z= 0.477 Chirality : 0.048 0.348 1592 Planarity : 0.006 0.055 798 Dihedral : 27.122 178.296 3785 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.90 % Allowed : 17.00 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.11 (0.37), residues: 397 helix: -1.61 (0.43), residues: 117 sheet: -2.94 (0.54), residues: 68 loop : -1.99 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 161 HIS 0.025 0.003 HIS D 22 PHE 0.023 0.003 PHE D 318 TYR 0.026 0.003 TYR D 388 ARG 0.009 0.001 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: D 94 MET cc_start: 0.5461 (tpt) cc_final: 0.5235 (tpt) REVERT: D 338 ASP cc_start: 0.6759 (OUTLIER) cc_final: 0.6463 (m-30) outliers start: 17 outliers final: 7 residues processed: 87 average time/residue: 0.2561 time to fit residues: 28.5178 Evaluate side-chains 61 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 494 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.0570 chunk 56 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 ASN ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 1.0139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.216 8782 Z= 0.521 Angle : 1.047 16.604 12957 Z= 0.541 Chirality : 0.056 0.566 1592 Planarity : 0.007 0.040 798 Dihedral : 26.715 176.064 3781 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 5.19 % Allowed : 18.44 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.00 (0.37), residues: 397 helix: -1.64 (0.41), residues: 112 sheet: -2.06 (0.58), residues: 72 loop : -2.15 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.004 TRP D 478 HIS 0.022 0.005 HIS D 333 PHE 0.032 0.004 PHE D 329 TYR 0.023 0.004 TYR D 387 ARG 0.023 0.002 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 45 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.7967 (p) REVERT: D 113 ARG cc_start: 0.7366 (mtt180) cc_final: 0.6780 (mtt180) REVERT: D 148 LYS cc_start: 0.7165 (tptt) cc_final: 0.6166 (ptmt) REVERT: D 167 ASN cc_start: 0.7349 (t0) cc_final: 0.7025 (t0) REVERT: D 309 GLN cc_start: 0.7654 (mp10) cc_final: 0.7359 (mp10) REVERT: D 372 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7296 (mmt180) outliers start: 18 outliers final: 6 residues processed: 82 average time/residue: 0.2234 time to fit residues: 24.3847 Evaluate side-chains 58 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 192 GLU Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN D 369 GLN ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 1.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 8782 Z= 0.330 Angle : 0.754 11.346 12957 Z= 0.399 Chirality : 0.044 0.482 1592 Planarity : 0.006 0.039 798 Dihedral : 26.314 174.941 3780 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.32 % Allowed : 19.31 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.39 (0.38), residues: 397 helix: -1.05 (0.42), residues: 120 sheet: -1.93 (0.66), residues: 60 loop : -1.78 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 478 HIS 0.005 0.002 HIS D 333 PHE 0.016 0.002 PHE D 370 TYR 0.018 0.002 TYR D 340 ARG 0.006 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.543 Fit side-chains REVERT: D 1 MET cc_start: 0.7374 (mmp) cc_final: 0.7108 (mmm) REVERT: D 84 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7255 (mm-30) REVERT: D 106 ARG cc_start: 0.7357 (ttp80) cc_final: 0.6879 (ttt90) REVERT: D 406 THR cc_start: 0.8283 (m) cc_final: 0.7952 (p) REVERT: D 440 MET cc_start: 0.8186 (tpp) cc_final: 0.7910 (mmm) outliers start: 15 outliers final: 8 residues processed: 54 average time/residue: 0.2129 time to fit residues: 15.8467 Evaluate side-chains 43 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN D 369 GLN D 376 GLN ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 1.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8782 Z= 0.230 Angle : 0.654 8.853 12957 Z= 0.349 Chirality : 0.038 0.305 1592 Planarity : 0.004 0.029 798 Dihedral : 26.031 175.761 3780 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.02 % Allowed : 21.61 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.65 (0.40), residues: 397 helix: -0.20 (0.45), residues: 119 sheet: -1.49 (0.67), residues: 60 loop : -1.48 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 161 HIS 0.004 0.001 HIS D 368 PHE 0.015 0.002 PHE D 198 TYR 0.007 0.001 TYR D 387 ARG 0.003 0.001 ARG D 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.566 Fit side-chains REVERT: D 12 LYS cc_start: 0.8398 (tmtt) cc_final: 0.8195 (tmtt) REVERT: D 37 ARG cc_start: 0.7550 (ttp80) cc_final: 0.7149 (ttm110) REVERT: D 106 ARG cc_start: 0.7547 (ttp80) cc_final: 0.6818 (ttt90) REVERT: D 402 MET cc_start: 0.7528 (mmm) cc_final: 0.7307 (mmt) REVERT: D 403 ASP cc_start: 0.6801 (t0) cc_final: 0.6578 (t0) REVERT: D 406 THR cc_start: 0.8503 (m) cc_final: 0.8252 (p) outliers start: 7 outliers final: 5 residues processed: 53 average time/residue: 0.2169 time to fit residues: 15.8346 Evaluate side-chains 41 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 449 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN D 333 HIS D 369 GLN ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 1.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8782 Z= 0.279 Angle : 0.684 9.582 12957 Z= 0.367 Chirality : 0.039 0.298 1592 Planarity : 0.005 0.037 798 Dihedral : 25.947 176.956 3780 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.32 % Allowed : 21.04 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.47 (0.40), residues: 397 helix: 0.03 (0.46), residues: 118 sheet: -1.46 (0.61), residues: 70 loop : -1.36 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 161 HIS 0.011 0.002 HIS D 333 PHE 0.017 0.003 PHE D 329 TYR 0.009 0.001 TYR D 484 ARG 0.003 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 36 time to evaluate : 0.558 Fit side-chains REVERT: D 37 ARG cc_start: 0.7630 (ttp80) cc_final: 0.7070 (ttm110) REVERT: D 106 ARG cc_start: 0.7583 (ttp80) cc_final: 0.6876 (ttt90) REVERT: D 406 THR cc_start: 0.8775 (m) cc_final: 0.8554 (p) REVERT: D 411 GLU cc_start: 0.7708 (mp0) cc_final: 0.7317 (mp0) REVERT: D 440 MET cc_start: 0.8130 (mmm) cc_final: 0.7862 (mmm) outliers start: 15 outliers final: 12 residues processed: 45 average time/residue: 0.2194 time to fit residues: 13.8824 Evaluate side-chains 47 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 35 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN D 369 GLN ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 1.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8782 Z= 0.337 Angle : 0.734 11.976 12957 Z= 0.387 Chirality : 0.041 0.282 1592 Planarity : 0.005 0.041 798 Dihedral : 25.860 177.669 3780 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.03 % Allowed : 19.60 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.43 (0.39), residues: 397 helix: -0.04 (0.45), residues: 119 sheet: -1.04 (0.71), residues: 61 loop : -1.44 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 478 HIS 0.007 0.002 HIS D 333 PHE 0.020 0.003 PHE D 370 TYR 0.012 0.001 TYR D 5 ARG 0.004 0.001 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 36 time to evaluate : 0.546 Fit side-chains REVERT: D 37 ARG cc_start: 0.7597 (ttp80) cc_final: 0.7118 (ttm110) REVERT: D 106 ARG cc_start: 0.7791 (ttp80) cc_final: 0.7062 (ttt90) REVERT: D 402 MET cc_start: 0.7870 (mmm) cc_final: 0.7561 (mmt) REVERT: D 403 ASP cc_start: 0.6882 (t0) cc_final: 0.6557 (t0) REVERT: D 440 MET cc_start: 0.8252 (mmm) cc_final: 0.7953 (mmm) outliers start: 14 outliers final: 9 residues processed: 46 average time/residue: 0.2069 time to fit residues: 13.2385 Evaluate side-chains 41 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 449 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 HIS ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 1.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8782 Z= 0.365 Angle : 0.737 9.741 12957 Z= 0.389 Chirality : 0.042 0.278 1592 Planarity : 0.005 0.040 798 Dihedral : 25.790 177.073 3780 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.17 % Allowed : 21.33 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.42 (0.38), residues: 397 helix: -0.01 (0.45), residues: 117 sheet: -0.91 (0.69), residues: 61 loop : -1.49 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP D 161 HIS 0.010 0.002 HIS D 368 PHE 0.014 0.003 PHE D 79 TYR 0.013 0.002 TYR D 327 ARG 0.005 0.001 ARG D 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.558 Fit side-chains REVERT: D 106 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7051 (ttt90) REVERT: D 440 MET cc_start: 0.8179 (mmm) cc_final: 0.7970 (mmm) outliers start: 11 outliers final: 10 residues processed: 42 average time/residue: 0.2531 time to fit residues: 14.1098 Evaluate side-chains 39 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 29 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 GLN ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 1.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8782 Z= 0.220 Angle : 0.644 10.273 12957 Z= 0.342 Chirality : 0.037 0.256 1592 Planarity : 0.004 0.030 798 Dihedral : 25.654 176.458 3780 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.46 % Allowed : 21.90 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.18 (0.39), residues: 397 helix: 0.22 (0.46), residues: 118 sheet: -0.96 (0.70), residues: 60 loop : -1.30 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 161 HIS 0.005 0.001 HIS D 333 PHE 0.012 0.002 PHE D 370 TYR 0.008 0.001 TYR D 5 ARG 0.003 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 33 time to evaluate : 0.581 Fit side-chains REVERT: D 106 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7423 (ttp-170) REVERT: D 440 MET cc_start: 0.8197 (mmm) cc_final: 0.7981 (mmm) outliers start: 12 outliers final: 8 residues processed: 41 average time/residue: 0.1930 time to fit residues: 11.3465 Evaluate side-chains 37 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 29 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 430 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN D 369 GLN ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 1.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8782 Z= 0.195 Angle : 0.620 9.991 12957 Z= 0.332 Chirality : 0.036 0.246 1592 Planarity : 0.004 0.034 798 Dihedral : 25.586 175.617 3780 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.02 % Allowed : 22.77 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.91 (0.40), residues: 397 helix: 0.47 (0.47), residues: 118 sheet: -0.72 (0.69), residues: 61 loop : -1.16 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 161 HIS 0.004 0.001 HIS D 333 PHE 0.009 0.001 PHE D 370 TYR 0.012 0.001 TYR D 340 ARG 0.003 0.000 ARG D 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 0.611 Fit side-chains REVERT: D 106 ARG cc_start: 0.7646 (ttp80) cc_final: 0.7281 (ttp-170) outliers start: 7 outliers final: 6 residues processed: 33 average time/residue: 0.2112 time to fit residues: 9.9069 Evaluate side-chains 33 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 430 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 0.0050 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN D 369 GLN D 376 GLN ** D 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.122490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.087318 restraints weight = 13649.081| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.65 r_work: 0.3260 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 1.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8782 Z= 0.176 Angle : 0.605 12.586 12957 Z= 0.321 Chirality : 0.035 0.230 1592 Planarity : 0.004 0.036 798 Dihedral : 25.499 175.460 3780 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.59 % Allowed : 22.48 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.41), residues: 397 helix: 0.72 (0.47), residues: 118 sheet: -0.33 (0.71), residues: 61 loop : -1.02 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 161 HIS 0.003 0.001 HIS D 373 PHE 0.022 0.002 PHE D 329 TYR 0.006 0.001 TYR D 5 ARG 0.002 0.000 ARG D 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1905.51 seconds wall clock time: 35 minutes 16.00 seconds (2116.00 seconds total)