Starting phenix.real_space_refine on Sat Dec 28 09:50:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ctl_26994/12_2024/8ctl_26994_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ctl_26994/12_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/cci-nas-00/data/ceres_data/8ctl_26994/12_2024/8ctl_26994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ctl_26994/12_2024/8ctl_26994.map" model { file = "/net/cci-nas-00/data/ceres_data/8ctl_26994/12_2024/8ctl_26994_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ctl_26994/12_2024/8ctl_26994_neut.cif" } 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. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.62, per 1000 atoms: 0.69 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 - 3.00 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: 2.39 Conformation dependent library (CDL) restraints added in 405.8 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: 4.37 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: 3.37 Time building geometry restraints manager: 2.71 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: 0.00 - 2.17: 11629 2.17 - 4.35: 1182 4.35 - 6.52: 112 6.52 - 8.70: 21 8.70 - 10.87: 13 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 3.040 nonbonded pdb=" O2' G C 95 " pdb=" N2 G C 131 " model vdw 2.309 3.120 nonbonded pdb=" OD1 ASN D 154 " pdb=" O2' U C 125 " model vdw 2.321 3.040 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 3.040 ... (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 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: 1.330 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 25.750 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.500 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.542 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: 0.3226 time to fit residues: 50.9120 Evaluate side-chains 77 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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: 5.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 D 492 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5069 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 8782 Z= 0.298 Angle : 0.887 13.077 12957 Z= 0.456 Chirality : 0.046 0.365 1592 Planarity : 0.006 0.051 798 Dihedral : 27.186 179.845 3785 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.61 % Allowed : 17.00 % Favored : 78.39 % 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: -3.05 (0.37), residues: 397 helix: -1.41 (0.44), residues: 117 sheet: -2.89 (0.54), residues: 68 loop : -2.05 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 161 HIS 0.020 0.003 HIS D 22 PHE 0.023 0.003 PHE D 318 TYR 0.021 0.003 TYR D 388 ARG 0.007 0.001 ARG D 330 *********************** 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 89 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 94 MET cc_start: 0.5364 (tpt) cc_final: 0.5108 (tpt) REVERT: D 148 LYS cc_start: 0.5286 (tttt) cc_final: 0.5046 (tptt) REVERT: D 436 MET cc_start: 0.7153 (mmm) cc_final: 0.6805 (mmm) outliers start: 16 outliers final: 6 residues processed: 84 average time/residue: 0.2630 time to fit residues: 28.3661 Evaluate side-chains 59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 341 LEU Chi-restraints excluded: chain D residue 359 SER 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: 2.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 56 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 GLN D 153 ASN D 194 ASN D 300 ASN ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.8710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.131 8782 Z= 0.424 Angle : 0.997 17.604 12957 Z= 0.510 Chirality : 0.051 0.385 1592 Planarity : 0.007 0.036 798 Dihedral : 26.645 177.022 3781 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 5.48 % Allowed : 17.00 % Favored : 77.52 % 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: -2.77 (0.37), residues: 397 helix: -1.29 (0.41), residues: 112 sheet: -2.09 (0.56), residues: 78 loop : -2.03 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 478 HIS 0.018 0.004 HIS D 333 PHE 0.041 0.004 PHE D 329 TYR 0.023 0.003 TYR D 46 ARG 0.020 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 84 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.664 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 4 residues processed: 79 average time/residue: 0.1941 time to fit residues: 21.1586 Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 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 130 GLN D 194 ASN D 300 ASN D 369 GLN D 428 HIS ** D 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 1.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8782 Z= 0.398 Angle : 0.874 13.441 12957 Z= 0.445 Chirality : 0.045 0.327 1592 Planarity : 0.007 0.054 798 Dihedral : 26.392 176.563 3780 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 5.19 % Allowed : 16.71 % 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: -2.37 (0.38), residues: 397 helix: -1.08 (0.41), residues: 119 sheet: -2.02 (0.63), residues: 60 loop : -1.71 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP D 478 HIS 0.006 0.001 HIS D 368 PHE 0.022 0.004 PHE D 370 TYR 0.012 0.002 TYR D 484 ARG 0.006 0.001 ARG D 110 *********************** 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 61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.536 Fit side-chains REVERT: D 1 MET cc_start: 0.7469 (mmp) cc_final: 0.7229 (mmm) REVERT: D 440 MET cc_start: 0.8211 (tpp) cc_final: 0.7901 (mmm) outliers start: 18 outliers final: 8 residues processed: 55 average time/residue: 0.1949 time to fit residues: 15.2572 Evaluate side-chains 42 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 89 ASP Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 449 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 ASN D 376 GLN D 492 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 1.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8782 Z= 0.275 Angle : 0.697 8.858 12957 Z= 0.371 Chirality : 0.040 0.315 1592 Planarity : 0.005 0.036 798 Dihedral : 26.158 175.261 3780 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.17 % Allowed : 18.44 % Favored : 78.39 % 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: -1.64 (0.39), residues: 397 helix: 0.01 (0.46), residues: 118 sheet: -1.48 (0.67), residues: 60 loop : -1.61 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 161 HIS 0.005 0.001 HIS D 22 PHE 0.013 0.002 PHE D 370 TYR 0.008 0.001 TYR D 5 ARG 0.004 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 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.592 Fit side-chains REVERT: D 37 ARG cc_start: 0.7488 (ttp80) cc_final: 0.7167 (ttm110) REVERT: D 72 THR cc_start: 0.8153 (p) cc_final: 0.7950 (p) REVERT: D 149 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7084 (tt0) REVERT: D 492 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7915 (mm-40) outliers start: 11 outliers final: 6 residues processed: 46 average time/residue: 0.1750 time to fit residues: 11.9260 Evaluate side-chains 41 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 492 GLN Chi-restraints excluded: chain D residue 493 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.0010 chunk 14 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 333 HIS D 369 GLN ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 1.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8782 Z= 0.212 Angle : 0.648 8.398 12957 Z= 0.348 Chirality : 0.038 0.297 1592 Planarity : 0.005 0.037 798 Dihedral : 25.995 175.542 3780 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.17 % Allowed : 18.16 % Favored : 78.67 % 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: -1.12 (0.40), residues: 397 helix: 0.45 (0.47), residues: 119 sheet: -1.18 (0.68), residues: 60 loop : -1.29 (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 22 PHE 0.011 0.002 PHE D 370 TYR 0.024 0.001 TYR D 494 ARG 0.003 0.000 ARG D 330 *********************** 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 to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.475 Fit side-chains REVERT: D 37 ARG cc_start: 0.7381 (ttp80) cc_final: 0.7092 (ttm110) REVERT: D 403 ASP cc_start: 0.6597 (t0) cc_final: 0.6320 (t0) outliers start: 11 outliers final: 5 residues processed: 50 average time/residue: 0.1919 time to fit residues: 13.8076 Evaluate side-chains 38 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 426 VAL Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 494 TYR 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: 3.9990 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 369 GLN ** D 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 1.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8782 Z= 0.350 Angle : 0.768 11.963 12957 Z= 0.406 Chirality : 0.043 0.332 1592 Planarity : 0.006 0.041 798 Dihedral : 25.999 176.456 3780 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.31 % Allowed : 20.46 % Favored : 77.23 % 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: -1.16 (0.39), residues: 397 helix: 0.38 (0.46), residues: 118 sheet: -1.19 (0.62), residues: 70 loop : -1.27 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 478 HIS 0.016 0.002 HIS D 333 PHE 0.022 0.003 PHE D 329 TYR 0.014 0.002 TYR D 5 ARG 0.009 0.001 ARG D 330 *********************** 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 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.538 Fit side-chains REVERT: D 37 ARG cc_start: 0.7587 (ttp80) cc_final: 0.6987 (ttm110) REVERT: D 393 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8489 (pt) REVERT: D 403 ASP cc_start: 0.6669 (t0) cc_final: 0.6425 (t0) REVERT: D 440 MET cc_start: 0.8127 (mmm) cc_final: 0.7891 (mmm) outliers start: 8 outliers final: 6 residues processed: 48 average time/residue: 0.2258 time to fit residues: 14.8531 Evaluate side-chains 42 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 369 GLN Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 426 VAL 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: 0.7980 chunk 40 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 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: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 369 GLN ** D 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 1.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8782 Z= 0.306 Angle : 0.696 8.803 12957 Z= 0.373 Chirality : 0.041 0.309 1592 Planarity : 0.006 0.088 798 Dihedral : 25.862 178.621 3780 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.88 % Allowed : 20.46 % Favored : 76.66 % 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: -1.16 (0.39), residues: 397 helix: 0.44 (0.46), residues: 118 sheet: -0.97 (0.71), residues: 59 loop : -1.40 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 161 HIS 0.010 0.002 HIS D 333 PHE 0.013 0.002 PHE D 79 TYR 0.009 0.001 TYR D 5 ARG 0.004 0.001 ARG D 371 *********************** 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 46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.531 Fit side-chains REVERT: D 37 ARG cc_start: 0.7499 (ttp80) cc_final: 0.7081 (ttm110) REVERT: D 393 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8580 (pt) outliers start: 10 outliers final: 7 residues processed: 43 average time/residue: 0.2038 time to fit residues: 12.6302 Evaluate side-chains 38 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 449 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 GLN ** D 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 1.4164 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= 0.257 Angle : 0.673 13.256 12957 Z= 0.360 Chirality : 0.039 0.294 1592 Planarity : 0.005 0.063 798 Dihedral : 25.795 179.037 3780 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.31 % Allowed : 21.90 % Favored : 75.79 % 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: -1.08 (0.39), residues: 397 helix: 0.59 (0.47), residues: 118 sheet: -1.03 (0.64), residues: 67 loop : -1.37 (0.37), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 478 HIS 0.005 0.001 HIS D 368 PHE 0.011 0.002 PHE D 79 TYR 0.009 0.001 TYR D 5 ARG 0.010 0.001 ARG D 106 *********************** 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 to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.513 Fit side-chains REVERT: D 37 ARG cc_start: 0.7404 (ttp80) cc_final: 0.7037 (ttm110) REVERT: D 106 ARG cc_start: 0.7384 (ttp-170) cc_final: 0.7179 (ttt90) REVERT: D 330 ARG cc_start: 0.8822 (ttm110) cc_final: 0.8387 (ttm110) REVERT: D 393 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8593 (pt) outliers start: 8 outliers final: 5 residues processed: 42 average time/residue: 0.2551 time to fit residues: 14.3895 Evaluate side-chains 39 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 140 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 426 VAL 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: 1.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 HIS D 369 GLN ** D 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 1.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8782 Z= 0.303 Angle : 0.695 9.313 12957 Z= 0.372 Chirality : 0.041 0.290 1592 Planarity : 0.006 0.072 798 Dihedral : 25.804 179.969 3780 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.31 % Allowed : 21.90 % Favored : 75.79 % 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: -1.12 (0.39), residues: 397 helix: 0.52 (0.47), residues: 118 sheet: -1.12 (0.65), residues: 67 loop : -1.34 (0.36), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP D 478 HIS 0.012 0.002 HIS D 339 PHE 0.010 0.002 PHE D 329 TYR 0.009 0.001 TYR D 484 ARG 0.010 0.001 ARG D 106 ********************** 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 41 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.495 Fit side-chains REVERT: D 37 ARG cc_start: 0.7417 (ttp80) cc_final: 0.7062 (ttm110) REVERT: D 106 ARG cc_start: 0.7405 (ttp-170) cc_final: 0.6958 (ttt90) REVERT: D 330 ARG cc_start: 0.8806 (ttm110) cc_final: 0.8582 (ttm110) REVERT: D 393 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8619 (pt) outliers start: 8 outliers final: 5 residues processed: 41 average time/residue: 0.2498 time to fit residues: 13.6359 Evaluate side-chains 38 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 140 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 GLN D 467 ASN ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.120250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.084793 restraints weight = 13671.588| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.65 r_work: 0.3217 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 1.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8782 Z= 0.223 Angle : 0.644 8.891 12957 Z= 0.348 Chirality : 0.038 0.269 1592 Planarity : 0.005 0.050 798 Dihedral : 25.744 179.479 3780 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.02 % Allowed : 22.19 % Favored : 75.79 % 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: -1.02 (0.39), residues: 397 helix: 0.59 (0.47), residues: 118 sheet: -1.07 (0.65), residues: 67 loop : -1.27 (0.37), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 161 HIS 0.007 0.002 HIS D 333 PHE 0.010 0.002 PHE D 79 TYR 0.007 0.001 TYR D 5 ARG 0.008 0.001 ARG D 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1777.38 seconds wall clock time: 33 minutes 19.52 seconds (1999.52 seconds total)