Starting phenix.real_space_refine on Tue Apr 9 01:23:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2r_40985/04_2024/8t2r_40985_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2r_40985/04_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_40985/04_2024/8t2r_40985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2r_40985/04_2024/8t2r_40985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2r_40985/04_2024/8t2r_40985_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2r_40985/04_2024/8t2r_40985_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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 Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 164": "OD1" <-> "OD2" Residue "D GLU 251": "OE1" <-> "OE2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D ASP 418": "OD1" <-> "OD2" Residue "D TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 9.97, per 1000 atoms: 0.66 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.56 Conformation dependent library (CDL) restraints added in 1.3 seconds 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... running ksdssp... Secondary structure from input PDB file: 20 helices and 2 sheets defined 60.8% alpha, 6.2% beta 177 base pairs and 312 stacking pairs defined. Time for finding SS restraints: 8.78 Creating SS restraints... Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 37 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 85 through 98 Processing helix chain 'D' and resid 102 through 105 No H-bonds generated for 'chain 'D' and resid 102 through 105' Processing helix chain 'D' and resid 119 through 131 Processing helix chain 'D' and resid 145 through 148 No H-bonds generated for 'chain 'D' and resid 145 through 148' Processing helix chain 'D' and resid 151 through 161 Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 198 through 217 removed outlier: 4.126A pdb=" N LEU D 210 " --> pdb=" O MET D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 251 Processing helix chain 'D' and resid 292 through 305 Processing helix chain 'D' and resid 314 through 332 Processing helix chain 'D' and resid 338 through 360 Processing helix chain 'D' and resid 363 through 373 Processing helix chain 'D' and resid 377 through 384 removed outlier: 4.381A pdb=" N AARG D 382 " --> pdb=" O ASN D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 395 Processing helix chain 'D' and resid 398 through 402 Processing helix chain 'D' and resid 405 through 410 Processing helix chain 'D' and resid 416 through 423 Processing sheet with id= A, first strand: chain 'D' and resid 263 through 265 removed outlier: 4.254A pdb=" N CYS D 228 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN D 220 " --> pdb=" O MET D 231 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 275 through 279 173 hydrogen bonds defined for protein. 513 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: 7.67 Time building geometry restraints manager: 9.12 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: 95.00 - 105.23: 2671 105.23 - 115.46: 11777 115.46 - 125.69: 8558 125.69 - 135.92: 2057 135.92 - 146.15: 3 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: 1632 2.72 - 3.26: 12290 3.26 - 3.81: 32651 3.81 - 4.35: 39458 4.35 - 4.90: 50695 Nonbonded interactions: 136726 Sorted by model distance: nonbonded pdb=" O2' A B 370 " pdb=" O4' G B 371 " model vdw 2.174 2.440 nonbonded pdb=" O2' G B 136 " pdb=" OP1 U B 148 " model vdw 2.239 2.440 nonbonded pdb=" OG SER D 415 " pdb=" OD2 ASP D 418 " model vdw 2.285 2.440 nonbonded pdb=" OP2 A B 137 " pdb=" O2' A B 147 " model vdw 2.290 2.440 nonbonded pdb=" OG SER D 110 " pdb=" OD2 ASP D 211 " model vdw 2.295 2.440 ... (remaining 136721 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.980 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: 12.430 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 53.040 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.150 ------------------------------------------------------------------------------- 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= 0.337 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 fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.748 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: 0.3381 time to fit residues: 18.3934 Evaluate side-chains 33 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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: 0.7980 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16531 Z= 0.271 Angle : 0.655 8.875 25066 Z= 0.329 Chirality : 0.036 0.303 3232 Planarity : 0.005 0.080 1108 Dihedral : 25.095 178.756 8912 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.66 % Favored : 95.81 % Rotamer: Outliers : 2.88 % Allowed : 22.48 % Favored : 74.64 % 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: -0.57 (0.39), residues: 394 helix: 0.33 (0.29), residues: 272 sheet: -0.80 (1.09), residues: 22 loop : -2.06 (0.54), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 136 HIS 0.003 0.001 HIS D 284 PHE 0.009 0.002 PHE D 145 TYR 0.020 0.002 TYR D 385 ARG 0.006 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 33 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.748 Fit side-chains REVERT: D 88 ARG cc_start: 0.7505 (ttm110) cc_final: 0.6821 (mtm110) REVERT: D 105 GLN cc_start: 0.8174 (tt0) cc_final: 0.7970 (tp40) REVERT: D 197 ASN cc_start: 0.6494 (t0) cc_final: 0.6049 (t0) REVERT: D 216 LYS cc_start: 0.8661 (tmtt) cc_final: 0.8272 (tttt) REVERT: D 247 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7537 (tmm-80) outliers start: 6 outliers final: 5 residues processed: 29 average time/residue: 0.3497 time to fit residues: 14.6932 Evaluate side-chains 30 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 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: 0.9980 chunk 67 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16531 Z= 0.316 Angle : 0.669 7.678 25066 Z= 0.336 Chirality : 0.037 0.288 3232 Planarity : 0.005 0.078 1108 Dihedral : 24.978 177.912 8912 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.19 % Favored : 95.29 % Rotamer: Outliers : 4.61 % Allowed : 21.90 % 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: 0.05 (0.41), residues: 394 helix: 0.85 (0.31), residues: 272 sheet: -0.71 (1.07), residues: 22 loop : -1.96 (0.57), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 136 HIS 0.003 0.001 HIS D 107 PHE 0.014 0.002 PHE D 145 TYR 0.020 0.002 TYR D 385 ARG 0.003 0.000 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 37 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 25 time to evaluate : 0.648 Fit side-chains REVERT: D 88 ARG cc_start: 0.7392 (ttm110) cc_final: 0.6688 (mtp180) REVERT: D 216 LYS cc_start: 0.8656 (tmtt) cc_final: 0.8269 (tttt) REVERT: D 247 ARG cc_start: 0.8162 (ttp80) cc_final: 0.7582 (tmm-80) outliers start: 12 outliers final: 9 residues processed: 33 average time/residue: 0.3149 time to fit residues: 15.1824 Evaluate side-chains 34 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 25 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET 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 399 VAL 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: 3.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 16531 Z= 0.442 Angle : 0.749 7.833 25066 Z= 0.374 Chirality : 0.041 0.312 3232 Planarity : 0.006 0.079 1108 Dihedral : 24.998 175.885 8912 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.71 % Favored : 94.76 % Rotamer: Outliers : 5.48 % Allowed : 21.90 % Favored : 72.62 % 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: -0.09 (0.41), residues: 394 helix: 0.78 (0.31), residues: 272 sheet: -0.88 (0.94), residues: 28 loop : -2.17 (0.54), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 136 HIS 0.003 0.001 HIS D 107 PHE 0.013 0.002 PHE D 145 TYR 0.024 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 43 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 28 time to evaluate : 1.150 Fit side-chains REVERT: D 88 ARG cc_start: 0.7474 (ttm110) cc_final: 0.6981 (mtm110) REVERT: D 216 LYS cc_start: 0.8600 (tmtt) cc_final: 0.8283 (tttt) REVERT: D 247 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7539 (tmm-80) REVERT: D 396 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8309 (pttm) outliers start: 15 outliers final: 12 residues processed: 37 average time/residue: 0.3378 time to fit residues: 17.8644 Evaluate side-chains 41 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 28 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET 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 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: 2.9990 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 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: 5.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16531 Z= 0.256 Angle : 0.616 7.312 25066 Z= 0.310 Chirality : 0.034 0.287 3232 Planarity : 0.005 0.080 1108 Dihedral : 24.867 177.272 8912 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.66 % Favored : 95.81 % Rotamer: Outliers : 4.90 % Allowed : 21.90 % 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: 0.43 (0.41), residues: 394 helix: 1.17 (0.31), residues: 272 sheet: -0.69 (1.02), residues: 22 loop : -1.90 (0.57), residues: 100 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 0.013 0.002 PHE D 145 TYR 0.021 0.002 TYR D 385 ARG 0.004 0.000 ARG D 247 *********************** 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 42 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 29 time to evaluate : 0.653 Fit side-chains REVERT: D 88 ARG cc_start: 0.7441 (ttm110) cc_final: 0.6959 (mtm110) REVERT: D 216 LYS cc_start: 0.8603 (tmtt) cc_final: 0.8234 (tttt) REVERT: D 236 MET cc_start: 0.5886 (ttp) cc_final: 0.5642 (ttp) REVERT: D 243 ARG cc_start: 0.7479 (ttp-110) cc_final: 0.7156 (mtm110) REVERT: D 247 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7548 (tmm-80) REVERT: D 396 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8018 (pttp) outliers start: 13 outliers final: 10 residues processed: 38 average time/residue: 0.3626 time to fit residues: 19.1593 Evaluate side-chains 40 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 29 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain D residue 399 VAL 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: 1.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 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 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8247 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16531 Z= 0.331 Angle : 0.665 7.882 25066 Z= 0.333 Chirality : 0.036 0.274 3232 Planarity : 0.005 0.081 1108 Dihedral : 24.840 176.914 8912 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.45 % Favored : 95.03 % Rotamer: Outliers : 5.19 % Allowed : 22.48 % Favored : 72.33 % 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: 0.49 (0.41), residues: 394 helix: 1.23 (0.31), residues: 272 sheet: -0.66 (0.99), residues: 22 loop : -1.94 (0.56), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 136 HIS 0.002 0.001 HIS D 107 PHE 0.010 0.002 PHE D 298 TYR 0.024 0.002 TYR D 385 ARG 0.005 0.001 ARG D 353 *********************** 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 44 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 30 time to evaluate : 0.763 Fit side-chains REVERT: D 88 ARG cc_start: 0.7462 (ttm110) cc_final: 0.6979 (mtm110) REVERT: D 216 LYS cc_start: 0.8621 (tmtt) cc_final: 0.8255 (tttt) REVERT: D 247 ARG cc_start: 0.8167 (ttp80) cc_final: 0.7557 (tmm-80) REVERT: D 396 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8107 (pttp) outliers start: 14 outliers final: 11 residues processed: 40 average time/residue: 0.3289 time to fit residues: 18.6911 Evaluate side-chains 41 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 29 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 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 386 THR Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain D residue 399 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.8980 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: 0.2980 chunk 52 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16531 Z= 0.309 Angle : 0.649 7.431 25066 Z= 0.326 Chirality : 0.036 0.271 3232 Planarity : 0.005 0.079 1108 Dihedral : 24.852 177.060 8912 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.93 % Favored : 95.55 % 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: 0.52 (0.41), residues: 394 helix: 1.26 (0.31), residues: 272 sheet: -0.68 (1.00), residues: 22 loop : -1.93 (0.55), 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 284 PHE 0.010 0.002 PHE D 145 TYR 0.022 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 41 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 29 time to evaluate : 0.719 Fit side-chains REVERT: D 88 ARG cc_start: 0.7478 (ttm110) cc_final: 0.6997 (mtm110) REVERT: D 216 LYS cc_start: 0.8630 (tmtt) cc_final: 0.8267 (tttt) REVERT: D 247 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7550 (tmm-80) outliers start: 12 outliers final: 11 residues processed: 37 average time/residue: 0.3401 time to fit residues: 18.0831 Evaluate side-chains 40 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 29 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 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 386 THR 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: 0.5980 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: 1.9990 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: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2882 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= 0.286 Angle : 0.634 7.389 25066 Z= 0.318 Chirality : 0.035 0.264 3232 Planarity : 0.005 0.080 1108 Dihedral : 24.837 177.252 8912 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.19 % Favored : 95.29 % Rotamer: Outliers : 4.32 % Allowed : 22.48 % 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: 0.58 (0.42), residues: 394 helix: 1.30 (0.31), residues: 272 sheet: -0.70 (1.00), residues: 22 loop : -1.91 (0.55), 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 0.009 0.002 PHE D 275 TYR 0.021 0.002 TYR D 385 ARG 0.004 0.001 ARG D 353 *********************** 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 39 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 28 time to evaluate : 0.694 Fit side-chains REVERT: D 88 ARG cc_start: 0.7482 (ttm110) cc_final: 0.6820 (mtp180) REVERT: D 216 LYS cc_start: 0.8616 (tmtt) cc_final: 0.8250 (tttt) REVERT: D 247 ARG cc_start: 0.8145 (ttp80) cc_final: 0.7538 (tmm-80) outliers start: 11 outliers final: 11 residues processed: 35 average time/residue: 0.3305 time to fit residues: 16.8130 Evaluate side-chains 39 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 28 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 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 386 THR Chi-restraints excluded: chain D residue 399 VAL 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: 0.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16531 Z= 0.330 Angle : 0.659 7.529 25066 Z= 0.330 Chirality : 0.036 0.270 3232 Planarity : 0.005 0.080 1108 Dihedral : 24.823 177.025 8912 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.45 % Favored : 95.03 % 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: 0.49 (0.41), residues: 394 helix: 1.24 (0.31), residues: 272 sheet: -0.68 (0.99), residues: 22 loop : -1.95 (0.55), 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 0.010 0.002 PHE D 298 TYR 0.023 0.002 TYR D 385 ARG 0.004 0.001 ARG D 353 *********************** 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 39 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 28 time to evaluate : 0.710 Fit side-chains REVERT: D 88 ARG cc_start: 0.7491 (ttm110) cc_final: 0.6833 (mtp180) REVERT: D 216 LYS cc_start: 0.8620 (tmtt) cc_final: 0.8256 (tttt) REVERT: D 247 ARG cc_start: 0.8150 (ttp80) cc_final: 0.7542 (tmm-80) outliers start: 11 outliers final: 11 residues processed: 35 average time/residue: 0.3415 time to fit residues: 17.0935 Evaluate side-chains 39 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 28 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 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 386 THR 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: 3.9990 chunk 91 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16531 Z= 0.383 Angle : 0.698 7.636 25066 Z= 0.348 Chirality : 0.038 0.290 3232 Planarity : 0.005 0.079 1108 Dihedral : 24.881 176.697 8912 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.45 % Favored : 95.03 % Rotamer: Outliers : 4.61 % Allowed : 22.48 % 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: 0.38 (0.41), residues: 394 helix: 1.15 (0.31), residues: 272 sheet: -0.72 (0.98), residues: 22 loop : -1.96 (0.55), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 136 HIS 0.003 0.001 HIS D 107 PHE 0.010 0.002 PHE D 145 TYR 0.024 0.002 TYR D 385 ARG 0.005 0.001 ARG D 353 ********************** 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 39 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 27 time to evaluate : 0.721 Fit side-chains REVERT: D 88 ARG cc_start: 0.7502 (ttm110) cc_final: 0.7044 (mtm110) REVERT: D 216 LYS cc_start: 0.8612 (tmtt) cc_final: 0.8280 (tttt) REVERT: D 247 ARG cc_start: 0.8145 (ttp80) cc_final: 0.7532 (tmm-80) outliers start: 12 outliers final: 11 residues processed: 34 average time/residue: 0.3361 time to fit residues: 16.6417 Evaluate side-chains 38 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 27 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 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 386 THR 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: 2.9990 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.177570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.125884 restraints weight = 38895.792| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.69 r_work: 0.3120 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16531 Z= 0.266 Angle : 0.640 7.206 25066 Z= 0.323 Chirality : 0.035 0.276 3232 Planarity : 0.005 0.080 1108 Dihedral : 24.906 177.097 8912 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.19 % Favored : 95.29 % Rotamer: Outliers : 4.32 % Allowed : 22.48 % 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: 0.52 (0.42), residues: 394 helix: 1.26 (0.31), residues: 272 sheet: -0.86 (0.96), residues: 28 loop : -1.97 (0.55), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 136 HIS 0.002 0.001 HIS D 284 PHE 0.010 0.002 PHE D 275 TYR 0.021 0.002 TYR D 385 ARG 0.003 0.001 ARG D 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2137.44 seconds wall clock time: 40 minutes 44.24 seconds (2444.24 seconds total)