Starting phenix.real_space_refine on Sun Nov 17 23:45:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2r_40985/11_2024/8t2r_40985.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2r_40985/11_2024/8t2r_40985.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/8t2r_40985/11_2024/8t2r_40985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2r_40985/11_2024/8t2r_40985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2r_40985/11_2024/8t2r_40985.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2r_40985/11_2024/8t2r_40985.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: 6 Type Number sf(0) Gaussians Ca 13 9.91 5 P 552 5.49 5 S 21 5.16 5 C 7314 2.51 5 N 2782 2.21 5 O 4381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 15063 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 3184 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 388, 3142 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 10, 'TRANS': 377} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 388, 3142 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 10, 'TRANS': 377} Chain breaks: 2 bond proxies already assigned to first conformer: 3149 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 3, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 3} Chain: "B" Number of atoms: 11724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 11724 Classifications: {'RNA': 545} Modifications used: {'rna2p_pur': 39, 'rna2p_pyr': 10, 'rna3p_pur': 291, 'rna3p_pyr': 205} Link IDs: {'rna2p': 48, 'rna3p': 496} Chain breaks: 6 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' CA': 13, 'NH4': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG D 347 " occ=0.25 ... (20 atoms not shown) pdb=" NH2BARG D 347 " occ=0.75 residue: pdb=" N AGLN D 359 " occ=0.72 ... (16 atoms not shown) pdb=" NE2BGLN D 359 " occ=0.28 residue: pdb=" N AARG D 382 " occ=0.67 ... (20 atoms not shown) pdb=" NH2BARG D 382 " occ=0.33 residue: pdb=" N AARG D 407 " occ=0.48 ... (20 atoms not shown) pdb=" NH2BARG D 407 " occ=0.52 Time building chain proxies: 7.71, per 1000 atoms: 0.51 Number of scatterers: 15063 At special positions: 0 Unit cell: (97.904, 134.196, 160.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 13 19.99 S 21 16.00 P 552 15.00 O 4381 8.00 N 2782 7.00 C 7314 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: 4.33 Conformation dependent library (CDL) restraints added in 845.7 milliseconds 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 736 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 2 sheets defined 70.9% alpha, 5.9% beta 177 base pairs and 312 stacking pairs defined. Time for finding SS restraints: 6.85 Creating SS restraints... Processing helix chain 'D' and resid 4 through 11 Processing helix chain 'D' and resid 12 through 27 Processing helix chain 'D' and resid 36 through 57 removed outlier: 6.619A pdb=" N GLU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 118 through 132 removed outlier: 3.601A pdb=" N ALA D 122 " --> pdb=" O CYS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 150 through 162 removed outlier: 3.589A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.681A pdb=" N ILE D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 218 removed outlier: 4.304A pdb=" N LEU D 201 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU D 210 " --> pdb=" O MET D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 252 Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 313 through 333 Processing helix chain 'D' and resid 337 through 361 removed outlier: 3.658A pdb=" N LYS D 361 " --> pdb=" O TRP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 374 Processing helix chain 'D' and resid 376 through 385 removed outlier: 4.381A pdb=" N AARG D 382 " --> pdb=" O ASN D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 396 removed outlier: 4.032A pdb=" N LYS D 396 " --> pdb=" O TYR D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 415 through 424 Processing sheet with id=AA1, first strand: chain 'D' and resid 220 through 224 removed outlier: 4.374A pdb=" N ASN D 220 " --> pdb=" O MET D 231 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N CYS D 228 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 275 through 279 205 hydrogen bonds defined for protein. 613 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 439 hydrogen bonds 692 hydrogen bond angles 0 basepair planarities 177 basepair parallelities 312 stacking parallelities Total time for adding SS restraints: 8.04 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1878 1.33 - 1.45: 7659 1.45 - 1.57: 5863 1.57 - 1.69: 1096 1.69 - 1.82: 35 Bond restraints: 16531 Sorted by residual: bond pdb=" C ASP D 265 " pdb=" N ARG D 266 " ideal model delta sigma weight residual 1.335 1.250 0.084 3.04e-02 1.08e+03 7.69e+00 bond pdb=" CB MET D 354 " pdb=" CG MET D 354 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.90e+00 bond pdb=" SD MET D 354 " pdb=" CE MET D 354 " ideal model delta sigma weight residual 1.791 1.743 0.048 2.50e-02 1.60e+03 3.75e+00 bond pdb=" C2' A B 370 " pdb=" O2' A B 370 " ideal model delta sigma weight residual 1.420 1.395 0.025 1.50e-02 4.44e+03 2.82e+00 bond pdb=" SD MET D 337 " pdb=" CE MET D 337 " ideal model delta sigma weight residual 1.791 1.749 0.042 2.50e-02 1.60e+03 2.78e+00 ... (remaining 16526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 24936 4.84 - 9.68: 125 9.68 - 14.52: 4 14.52 - 19.36: 0 19.36 - 24.20: 1 Bond angle restraints: 25066 Sorted by residual: angle pdb=" C ASP D 265 " pdb=" N ARG D 266 " pdb=" CA ARG D 266 " ideal model delta sigma weight residual 121.95 146.15 -24.20 3.74e+00 7.15e-02 4.19e+01 angle pdb=" C ALA D 225 " pdb=" N ASP D 226 " pdb=" CA ASP D 226 " ideal model delta sigma weight residual 122.61 131.23 -8.62 1.56e+00 4.11e-01 3.05e+01 angle pdb=" O3' C B 206 " pdb=" C3' C B 206 " pdb=" C2' C B 206 " ideal model delta sigma weight residual 113.70 121.28 -7.58 1.50e+00 4.44e-01 2.56e+01 angle pdb=" C3' A B 67 " pdb=" O3' A B 67 " pdb=" P U B 68 " ideal model delta sigma weight residual 120.20 127.49 -7.29 1.50e+00 4.44e-01 2.36e+01 angle pdb=" O3' U B 46 " pdb=" C3' U B 46 " pdb=" C2' U B 46 " ideal model delta sigma weight residual 113.70 120.78 -7.08 1.50e+00 4.44e-01 2.23e+01 ... (remaining 25061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 8939 35.34 - 70.68: 1356 70.68 - 106.02: 158 106.02 - 141.36: 8 141.36 - 176.70: 9 Dihedral angle restraints: 10470 sinusoidal: 9325 harmonic: 1145 Sorted by residual: dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N ILE D 101 " pdb=" CA ILE D 101 " ideal model delta harmonic sigma weight residual -180.00 -128.31 -51.69 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" O4' C B 138 " pdb=" C1' C B 138 " pdb=" N1 C B 138 " pdb=" C2 C B 138 " ideal model delta sinusoidal sigma weight residual -160.00 16.70 -176.70 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U B 361 " pdb=" C1' U B 361 " pdb=" N1 U B 361 " pdb=" C2 U B 361 " ideal model delta sinusoidal sigma weight residual 200.00 48.56 151.44 1 1.50e+01 4.44e-03 8.01e+01 ... (remaining 10467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2960 0.074 - 0.148: 241 0.148 - 0.221: 18 0.221 - 0.295: 6 0.295 - 0.369: 7 Chirality restraints: 3232 Sorted by residual: chirality pdb=" C1' A B 51 " pdb=" O4' A B 51 " pdb=" C2' A B 51 " pdb=" N9 A B 51 " both_signs ideal model delta sigma weight residual False 2.46 2.09 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C3' U B 46 " pdb=" C4' U B 46 " pdb=" O3' U B 46 " pdb=" C2' U B 46 " both_signs ideal model delta sigma weight residual False -2.48 -2.13 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C3' G B 348 " pdb=" C4' G B 348 " pdb=" O3' G B 348 " pdb=" C2' G B 348 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 3229 not shown) Planarity restraints: 1108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 99 " -0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO D 100 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A B 51 " 0.038 2.00e-02 2.50e+03 1.81e-02 9.05e+00 pdb=" N9 A B 51 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A B 51 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A B 51 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A B 51 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 51 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 51 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A B 51 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B 51 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 51 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A B 51 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 436 " 0.037 2.00e-02 2.50e+03 1.93e-02 8.37e+00 pdb=" N1 U B 436 " -0.040 2.00e-02 2.50e+03 pdb=" C2 U B 436 " -0.007 2.00e-02 2.50e+03 pdb=" O2 U B 436 " -0.000 2.00e-02 2.50e+03 pdb=" N3 U B 436 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U B 436 " 0.008 2.00e-02 2.50e+03 pdb=" O4 U B 436 " 0.012 2.00e-02 2.50e+03 pdb=" C5 U B 436 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 436 " -0.007 2.00e-02 2.50e+03 ... (remaining 1105 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1629 2.72 - 3.26: 12266 3.26 - 3.81: 32606 3.81 - 4.35: 39407 4.35 - 4.90: 50689 Nonbonded interactions: 136597 Sorted by model distance: nonbonded pdb=" O2' A B 370 " pdb=" O4' G B 371 " model vdw 2.174 3.040 nonbonded pdb=" O2' G B 136 " pdb=" OP1 U B 148 " model vdw 2.239 3.040 nonbonded pdb=" OG SER D 415 " pdb=" OD2 ASP D 418 " model vdw 2.285 3.040 nonbonded pdb=" OP2 A B 137 " pdb=" O2' A B 147 " model vdw 2.290 3.040 nonbonded pdb=" OG SER D 110 " pdb=" OD2 ASP D 211 " model vdw 2.295 3.040 ... (remaining 136592 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=0.00 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: 15.330 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 6.310 Process input model: 37.290 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.006 0.084 16531 Z= 0.335 Angle : 0.956 24.199 25066 Z= 0.456 Chirality : 0.045 0.369 3232 Planarity : 0.007 0.086 1108 Dihedral : 25.029 176.698 9734 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.14 % Favored : 96.34 % Rotamer: Outliers : 1.15 % Allowed : 23.34 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -2.13 (0.34), residues: 394 helix: -0.97 (0.26), residues: 272 sheet: -1.11 (1.04), residues: 20 loop : -2.29 (0.49), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 328 HIS 0.003 0.001 HIS D 284 PHE 0.018 0.003 PHE D 221 TYR 0.029 0.003 TYR D 350 ARG 0.005 0.001 ARG D 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.682 Fit side-chains REVERT: D 197 ASN cc_start: 0.6283 (t0) cc_final: 0.5914 (t0) REVERT: D 216 LYS cc_start: 0.8625 (tmtt) cc_final: 0.8217 (tttt) REVERT: D 236 MET cc_start: 0.5233 (ppp) cc_final: 0.4107 (ttp) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.3451 time to fit residues: 18.5104 Evaluate side-chains 33 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16531 Z= 0.274 Angle : 0.672 9.854 25066 Z= 0.339 Chirality : 0.036 0.313 3232 Planarity : 0.005 0.080 1108 Dihedral : 25.092 176.494 8912 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.40 % Favored : 96.07 % Rotamer: Outliers : 2.88 % Allowed : 22.77 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.24 (0.40), residues: 394 helix: 0.59 (0.30), residues: 273 sheet: -1.00 (1.02), residues: 22 loop : -1.91 (0.55), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 136 HIS 0.005 0.001 HIS D 284 PHE 0.012 0.002 PHE D 145 TYR 0.021 0.002 TYR D 385 ARG 0.007 0.001 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.766 Fit side-chains REVERT: D 88 ARG cc_start: 0.7436 (ttm110) cc_final: 0.6815 (mtm110) REVERT: D 105 GLN cc_start: 0.8173 (tt0) cc_final: 0.7949 (tp40) REVERT: D 197 ASN cc_start: 0.6360 (t0) cc_final: 0.5988 (t0) REVERT: D 216 LYS cc_start: 0.8719 (tmtt) cc_final: 0.8375 (tttt) REVERT: D 247 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7608 (tmm-80) outliers start: 6 outliers final: 6 residues processed: 32 average time/residue: 0.3366 time to fit residues: 15.7640 Evaluate side-chains 34 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 399 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16531 Z= 0.299 Angle : 0.668 8.579 25066 Z= 0.335 Chirality : 0.036 0.290 3232 Planarity : 0.005 0.079 1108 Dihedral : 24.954 177.428 8912 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.66 % Favored : 95.81 % Rotamer: Outliers : 4.32 % Allowed : 21.61 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.41), residues: 394 helix: 1.19 (0.31), residues: 273 sheet: -0.91 (0.99), residues: 22 loop : -1.86 (0.57), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 136 HIS 0.004 0.001 HIS D 107 PHE 0.013 0.002 PHE D 145 TYR 0.023 0.002 TYR D 385 ARG 0.004 0.001 ARG D 353 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.705 Fit side-chains REVERT: D 88 ARG cc_start: 0.7307 (ttm110) cc_final: 0.6616 (mtm110) REVERT: D 197 ASN cc_start: 0.6522 (t0) cc_final: 0.5974 (t0) REVERT: D 216 LYS cc_start: 0.8712 (tmtt) cc_final: 0.8335 (tttt) REVERT: D 247 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7604 (tmm-80) outliers start: 11 outliers final: 8 residues processed: 34 average time/residue: 0.3458 time to fit residues: 17.7555 Evaluate side-chains 36 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 379 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 23 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 16531 Z= 0.408 Angle : 0.743 7.765 25066 Z= 0.371 Chirality : 0.040 0.289 3232 Planarity : 0.005 0.080 1108 Dihedral : 24.953 176.798 8912 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.97 % Favored : 94.50 % Rotamer: Outliers : 5.48 % Allowed : 21.33 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 0.48 (0.41), residues: 394 helix: 1.25 (0.31), residues: 272 sheet: -0.83 (0.95), residues: 22 loop : -1.98 (0.56), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 136 HIS 0.004 0.001 HIS D 107 PHE 0.015 0.002 PHE D 145 TYR 0.025 0.002 TYR D 385 ARG 0.007 0.001 ARG D 353 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 26 time to evaluate : 0.614 Fit side-chains REVERT: D 88 ARG cc_start: 0.7317 (ttm110) cc_final: 0.6624 (mtm110) REVERT: D 216 LYS cc_start: 0.8686 (tmtt) cc_final: 0.8311 (tttt) REVERT: D 247 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7553 (tmm-80) REVERT: D 396 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8228 (pttm) outliers start: 15 outliers final: 11 residues processed: 37 average time/residue: 0.3384 time to fit residues: 18.3501 Evaluate side-chains 39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 399 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 36 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16531 Z= 0.278 Angle : 0.643 7.525 25066 Z= 0.324 Chirality : 0.035 0.284 3232 Planarity : 0.005 0.080 1108 Dihedral : 24.832 177.603 8912 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.93 % Favored : 95.55 % Rotamer: Outliers : 4.32 % Allowed : 21.90 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.42), residues: 394 helix: 1.49 (0.31), residues: 272 sheet: -0.83 (0.93), residues: 22 loop : -1.93 (0.57), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 136 HIS 0.003 0.001 HIS D 107 PHE 0.012 0.002 PHE D 145 TYR 0.023 0.002 TYR D 385 ARG 0.003 0.001 ARG D 353 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.711 Fit side-chains REVERT: D 88 ARG cc_start: 0.7296 (ttm110) cc_final: 0.6629 (mtm110) REVERT: D 216 LYS cc_start: 0.8732 (tmtt) cc_final: 0.8329 (tttt) REVERT: D 247 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7564 (tmm-80) REVERT: D 396 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8042 (pttp) outliers start: 11 outliers final: 9 residues processed: 36 average time/residue: 0.3311 time to fit residues: 17.3300 Evaluate side-chains 37 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 396 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 89 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16531 Z= 0.299 Angle : 0.656 7.505 25066 Z= 0.329 Chirality : 0.036 0.274 3232 Planarity : 0.005 0.080 1108 Dihedral : 24.789 177.238 8912 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.19 % Favored : 95.29 % Rotamer: Outliers : 4.61 % Allowed : 22.19 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 0.92 (0.42), residues: 394 helix: 1.61 (0.31), residues: 272 sheet: -0.88 (0.90), residues: 22 loop : -1.87 (0.58), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 136 HIS 0.003 0.001 HIS D 107 PHE 0.012 0.002 PHE D 145 TYR 0.024 0.002 TYR D 385 ARG 0.004 0.001 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.717 Fit side-chains REVERT: D 88 ARG cc_start: 0.7328 (ttm110) cc_final: 0.6637 (mtm110) REVERT: D 216 LYS cc_start: 0.8732 (tmtt) cc_final: 0.8330 (tttt) REVERT: D 247 ARG cc_start: 0.8213 (ttp80) cc_final: 0.7596 (tmm-80) REVERT: D 396 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8091 (pttp) outliers start: 12 outliers final: 9 residues processed: 37 average time/residue: 0.3296 time to fit residues: 17.6233 Evaluate side-chains 36 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 396 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 16531 Z= 0.349 Angle : 0.697 7.641 25066 Z= 0.349 Chirality : 0.038 0.277 3232 Planarity : 0.005 0.079 1108 Dihedral : 24.813 177.143 8912 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.45 % Favored : 95.03 % Rotamer: Outliers : 5.19 % Allowed : 21.33 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 0.80 (0.41), residues: 394 helix: 1.52 (0.31), residues: 272 sheet: -0.86 (0.89), residues: 22 loop : -1.92 (0.57), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 136 HIS 0.004 0.001 HIS D 107 PHE 0.013 0.002 PHE D 145 TYR 0.024 0.002 TYR D 385 ARG 0.004 0.001 ARG D 353 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.782 Fit side-chains REVERT: D 88 ARG cc_start: 0.7324 (ttm110) cc_final: 0.6672 (mtm110) REVERT: D 216 LYS cc_start: 0.8699 (tmtt) cc_final: 0.8465 (tttt) REVERT: D 396 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8204 (pttm) outliers start: 14 outliers final: 13 residues processed: 37 average time/residue: 0.3311 time to fit residues: 17.7332 Evaluate side-chains 40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 399 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16531 Z= 0.273 Angle : 0.654 7.430 25066 Z= 0.329 Chirality : 0.036 0.257 3232 Planarity : 0.005 0.080 1108 Dihedral : 24.826 176.830 8912 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.93 % Favored : 95.55 % Rotamer: Outliers : 4.90 % Allowed : 22.19 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 0.94 (0.42), residues: 394 helix: 1.61 (0.31), residues: 272 sheet: -0.84 (0.90), residues: 22 loop : -1.84 (0.59), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 136 HIS 0.002 0.001 HIS D 107 PHE 0.012 0.002 PHE D 145 TYR 0.023 0.002 TYR D 385 ARG 0.008 0.001 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.779 Fit side-chains REVERT: D 88 ARG cc_start: 0.7306 (ttm110) cc_final: 0.6665 (mtm110) REVERT: D 216 LYS cc_start: 0.8689 (tmtt) cc_final: 0.8450 (tttt) REVERT: D 247 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7676 (tmm-80) REVERT: D 396 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8117 (pttp) outliers start: 13 outliers final: 10 residues processed: 37 average time/residue: 0.3169 time to fit residues: 16.9241 Evaluate side-chains 38 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 396 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 16531 Z= 0.330 Angle : 0.682 7.666 25066 Z= 0.341 Chirality : 0.037 0.268 3232 Planarity : 0.005 0.078 1108 Dihedral : 24.789 177.441 8912 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.19 % Favored : 95.29 % Rotamer: Outliers : 5.19 % Allowed : 21.90 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.41), residues: 394 helix: 1.55 (0.31), residues: 272 sheet: -0.83 (0.87), residues: 22 loop : -1.93 (0.57), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 136 HIS 0.004 0.001 HIS D 107 PHE 0.012 0.002 PHE D 145 TYR 0.024 0.002 TYR D 385 ARG 0.006 0.001 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.712 Fit side-chains REVERT: D 88 ARG cc_start: 0.7315 (ttm110) cc_final: 0.6665 (mtm110) REVERT: D 216 LYS cc_start: 0.8699 (tmtt) cc_final: 0.8463 (tttt) REVERT: D 247 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7642 (tmm-80) REVERT: D 396 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8197 (pttm) outliers start: 14 outliers final: 13 residues processed: 37 average time/residue: 0.3279 time to fit residues: 17.5280 Evaluate side-chains 40 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 399 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 16531 Z= 0.455 Angle : 0.763 7.978 25066 Z= 0.379 Chirality : 0.041 0.301 3232 Planarity : 0.006 0.078 1108 Dihedral : 24.851 177.136 8912 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.71 % Favored : 94.76 % Rotamer: Outliers : 5.19 % Allowed : 21.90 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 0.60 (0.41), residues: 394 helix: 1.36 (0.31), residues: 272 sheet: -0.81 (0.88), residues: 22 loop : -1.99 (0.56), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 136 HIS 0.005 0.001 HIS D 107 PHE 0.013 0.002 PHE D 145 TYR 0.028 0.002 TYR D 385 ARG 0.006 0.001 ARG D 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.720 Fit side-chains REVERT: D 88 ARG cc_start: 0.7410 (ttm110) cc_final: 0.6733 (mtm110) REVERT: D 216 LYS cc_start: 0.8696 (tmtt) cc_final: 0.8359 (tttt) REVERT: D 396 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8281 (pttm) outliers start: 14 outliers final: 13 residues processed: 39 average time/residue: 0.3157 time to fit residues: 17.8974 Evaluate side-chains 43 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 334 ILE Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 399 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.179930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.125532 restraints weight = 38897.306| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.79 r_work: 0.3136 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16531 Z= 0.176 Angle : 0.606 7.455 25066 Z= 0.304 Chirality : 0.033 0.254 3232 Planarity : 0.005 0.080 1108 Dihedral : 24.753 176.347 8912 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.14 % Favored : 96.34 % Rotamer: Outliers : 4.32 % Allowed : 22.77 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 (0.42), residues: 394 helix: 1.67 (0.31), residues: 273 sheet: -1.02 (0.85), residues: 22 loop : -1.75 (0.60), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 136 HIS 0.001 0.000 HIS D 107 PHE 0.011 0.002 PHE D 145 TYR 0.017 0.002 TYR D 385 ARG 0.007 0.001 ARG D 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2199.51 seconds wall clock time: 43 minutes 13.17 seconds (2593.17 seconds total)