Starting phenix.real_space_refine on Fri Sep 27 01:08:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uim_26549/09_2024/7uim_26549.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uim_26549/09_2024/7uim_26549.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/7uim_26549/09_2024/7uim_26549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uim_26549/09_2024/7uim_26549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uim_26549/09_2024/7uim_26549.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uim_26549/09_2024/7uim_26549.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= 0.015 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 P 536 5.49 5 Mg 13 5.21 5 S 21 5.16 5 C 7184 2.51 5 N 2736 2.21 5 O 4282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14772 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 11624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 11624 Inner-chain residues flagged as termini: ['pdbres=" G B 171 "', 'pdbres=" G B 220 "', 'pdbres=" A B 298 "', 'pdbres=" A B 401 "', 'pdbres=" G B 551 "'] Classifications: {'RNA': 541} Modifications used: {'5*END': 5, 'rna2p_pur': 42, 'rna2p_pyr': 16, 'rna3p_pur': 286, 'rna3p_pyr': 197} Link IDs: {'rna2p': 57, 'rna3p': 483} Chain: "D" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3133 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 10, 'TRANS': 376} Chain breaks: 2 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' MG': 13, 'NH4': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Time building chain proxies: 9.22, per 1000 atoms: 0.62 Number of scatterers: 14772 At special positions: 0 Unit cell: (100.672, 153.92, 154.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 536 15.00 Mg 13 11.99 O 4282 8.00 N 2736 7.00 C 7184 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 556.8 milliseconds 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 724 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 2 sheets defined 72.4% alpha, 4.1% beta 159 base pairs and 290 stacking pairs defined. Time for finding SS restraints: 6.44 Creating SS restraints... Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 12 through 27 Processing helix chain 'D' and resid 36 through 58 removed outlier: 6.359A pdb=" N GLU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N THR D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 106 Proline residue: D 100 - end of helix removed outlier: 6.256A pdb=" N GLU D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 133 removed outlier: 3.649A 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 Processing helix chain 'D' and resid 164 through 177 removed outlier: 4.064A pdb=" N ILE D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 218 removed outlier: 3.870A 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 266 through 270 removed outlier: 3.566A pdb=" N LEU D 270 " --> pdb=" O PRO D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 313 through 332 Processing helix chain 'D' and resid 337 through 361 removed outlier: 4.159A pdb=" N GLU D 343 " --> pdb=" O THR D 339 " (cutoff:3.500A) removed outlier: 3.622A 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 387 Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'D' and resid 397 through 403 removed outlier: 3.732A pdb=" N ILE D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 412 Processing helix chain 'D' and resid 415 through 423 Processing sheet with id=AA1, first strand: chain 'D' and resid 220 through 223 removed outlier: 4.571A pdb=" N ASN D 220 " --> pdb=" O MET D 231 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP D 265 " --> pdb=" O ILE D 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 275 through 277 200 hydrogen bonds defined for protein. 591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 383 hydrogen bonds 574 hydrogen bond angles 0 basepair planarities 159 basepair parallelities 290 stacking parallelities Total time for adding SS restraints: 6.57 Time building geometry restraints manager: 3.73 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: 1918 1.33 - 1.45: 7477 1.45 - 1.57: 5712 1.57 - 1.70: 1072 1.70 - 1.82: 35 Bond restraints: 16214 Sorted by residual: bond pdb=" CB GLU D 39 " pdb=" CG GLU D 39 " ideal model delta sigma weight residual 1.520 1.578 -0.058 3.00e-02 1.11e+03 3.76e+00 bond pdb=" CB ILE D 325 " pdb=" CG2 ILE D 325 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.35e+00 bond pdb=" CD2 TYR D 174 " pdb=" CE2 TYR D 174 " ideal model delta sigma weight residual 1.382 1.329 0.053 3.00e-02 1.11e+03 3.16e+00 bond pdb=" CB LYS D 36 " pdb=" CG LYS D 36 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.60e+00 bond pdb=" CB ARG D 377 " pdb=" CG ARG D 377 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.48e+00 ... (remaining 16209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 24165 2.69 - 5.38: 368 5.38 - 8.08: 47 8.08 - 10.77: 6 10.77 - 13.46: 3 Bond angle restraints: 24589 Sorted by residual: angle pdb=" CA LYS D 36 " pdb=" CB LYS D 36 " pdb=" CG LYS D 36 " ideal model delta sigma weight residual 114.10 127.56 -13.46 2.00e+00 2.50e-01 4.53e+01 angle pdb=" CA PRO D 281 " pdb=" N PRO D 281 " pdb=" CD PRO D 281 " ideal model delta sigma weight residual 112.00 104.42 7.58 1.40e+00 5.10e-01 2.93e+01 angle pdb=" O3' G B 123 " pdb=" C3' G B 123 " pdb=" C2' G B 123 " ideal model delta sigma weight residual 113.70 121.42 -7.72 1.50e+00 4.44e-01 2.65e+01 angle pdb=" CA ARG D 377 " pdb=" CB ARG D 377 " pdb=" CG ARG D 377 " ideal model delta sigma weight residual 114.10 124.17 -10.07 2.00e+00 2.50e-01 2.54e+01 angle pdb=" CB LYS D 263 " pdb=" CG LYS D 263 " pdb=" CD LYS D 263 " ideal model delta sigma weight residual 111.30 121.59 -10.29 2.30e+00 1.89e-01 2.00e+01 ... (remaining 24584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.89: 8654 33.89 - 67.78: 1431 67.78 - 101.67: 157 101.67 - 135.57: 2 135.57 - 169.46: 6 Dihedral angle restraints: 10250 sinusoidal: 9126 harmonic: 1124 Sorted by residual: dihedral pdb=" O4' C B 439 " pdb=" C1' C B 439 " pdb=" N1 C B 439 " pdb=" C2 C B 439 " ideal model delta sinusoidal sigma weight residual 232.00 62.54 169.46 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" O4' C B 440 " pdb=" C1' C B 440 " pdb=" N1 C B 440 " pdb=" C2 C B 440 " ideal model delta sinusoidal sigma weight residual -128.00 35.88 -163.88 1 1.70e+01 3.46e-03 6.51e+01 dihedral pdb=" CA PRO D 281 " pdb=" C PRO D 281 " pdb=" N ARG D 282 " pdb=" CA ARG D 282 " ideal model delta harmonic sigma weight residual 180.00 148.62 31.38 0 5.00e+00 4.00e-02 3.94e+01 ... (remaining 10247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2769 0.062 - 0.124: 324 0.124 - 0.186: 56 0.186 - 0.248: 9 0.248 - 0.310: 7 Chirality restraints: 3165 Sorted by residual: chirality pdb=" C3' G B 123 " pdb=" C4' G B 123 " pdb=" O3' G B 123 " pdb=" C2' G B 123 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C3' G B 333 " pdb=" C4' G B 333 " pdb=" O3' G B 333 " pdb=" C2' G B 333 " both_signs ideal model delta sigma weight residual False -2.48 -2.19 -0.29 2.00e-01 2.50e+01 2.05e+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 -2.20 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 3162 not shown) Planarity restraints: 1084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 280 " -0.066 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO D 281 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO D 281 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 281 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 39 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" CD GLU D 39 " 0.058 2.00e-02 2.50e+03 pdb=" OE1 GLU D 39 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU D 39 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 289 " 0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO D 290 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 290 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 290 " 0.044 5.00e-02 4.00e+02 ... (remaining 1081 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 82 2.50 - 3.10: 9414 3.10 - 3.70: 29724 3.70 - 4.30: 41728 4.30 - 4.90: 53740 Nonbonded interactions: 134688 Sorted by model distance: nonbonded pdb=" OP1 C B 581 " pdb="MG MG B 701 " model vdw 1.903 2.170 nonbonded pdb=" O3' U B 638 " pdb="MG MG B 701 " model vdw 1.943 2.170 nonbonded pdb=" OP2 G B 158 " pdb="MG MG B 708 " model vdw 1.984 2.170 nonbonded pdb=" OP2 A B 560 " pdb="MG MG B 705 " model vdw 1.992 2.170 nonbonded pdb=" OP2 A B 323 " pdb="MG MG B 709 " model vdw 2.016 2.170 ... (remaining 134683 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: 4.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.500 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4534 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 : 0.005 0.068 16214 Z= 0.294 Angle : 0.871 13.462 24589 Z= 0.437 Chirality : 0.045 0.310 3165 Planarity : 0.007 0.096 1084 Dihedral : 24.926 169.458 9526 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 31.67 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.28 (0.39), residues: 381 helix: -0.58 (0.28), residues: 256 sheet: -1.65 (0.92), residues: 24 loop : -0.87 (0.60), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 360 HIS 0.007 0.002 HIS D 291 PHE 0.032 0.003 PHE D 298 TYR 0.032 0.003 TYR D 278 ARG 0.010 0.001 ARG D 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 26 ASN cc_start: 0.8204 (m-40) cc_final: 0.8002 (m-40) REVERT: D 175 LEU cc_start: 0.7673 (mt) cc_final: 0.7446 (tp) REVERT: D 270 LEU cc_start: 0.4275 (mt) cc_final: 0.2998 (mt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3581 time to fit residues: 60.5537 Evaluate side-chains 71 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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: 8.9990 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5558 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 16214 Z= 0.453 Angle : 1.016 10.520 24589 Z= 0.499 Chirality : 0.050 0.293 3165 Planarity : 0.007 0.080 1084 Dihedral : 25.843 175.120 8721 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 34.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 7.92 % Allowed : 30.50 % Favored : 61.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.38), residues: 381 helix: -0.58 (0.29), residues: 268 sheet: -1.17 (0.98), residues: 24 loop : -1.93 (0.55), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 328 HIS 0.008 0.002 HIS D 109 PHE 0.019 0.004 PHE D 298 TYR 0.025 0.003 TYR D 392 ARG 0.019 0.002 ARG D 172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 68 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 130 MET cc_start: 0.6662 (mpp) cc_final: 0.6161 (mpp) REVERT: D 310 TRP cc_start: 0.7278 (OUTLIER) cc_final: 0.6670 (t60) outliers start: 27 outliers final: 11 residues processed: 89 average time/residue: 0.2997 time to fit residues: 37.9460 Evaluate side-chains 67 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 414 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 107 HIS D 204 ASN D 244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5406 moved from start: 0.6579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16214 Z= 0.223 Angle : 0.686 10.660 24589 Z= 0.345 Chirality : 0.035 0.222 3165 Planarity : 0.005 0.062 1084 Dihedral : 25.398 168.869 8721 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 6.74 % Allowed : 28.15 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.41), residues: 381 helix: 0.15 (0.30), residues: 265 sheet: -0.40 (0.99), residues: 24 loop : -2.04 (0.58), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 328 HIS 0.008 0.002 HIS D 151 PHE 0.013 0.002 PHE D 146 TYR 0.015 0.002 TYR D 385 ARG 0.005 0.001 ARG D 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: D 173 LYS cc_start: 0.6821 (mmtm) cc_final: 0.5579 (mttt) REVERT: D 174 TYR cc_start: 0.6085 (OUTLIER) cc_final: 0.5505 (t80) REVERT: D 310 TRP cc_start: 0.7092 (OUTLIER) cc_final: 0.6296 (t60) REVERT: D 323 GLN cc_start: 0.6055 (OUTLIER) cc_final: 0.3863 (tm-30) REVERT: D 416 MET cc_start: 0.7897 (mmm) cc_final: 0.7569 (mmm) outliers start: 23 outliers final: 11 residues processed: 83 average time/residue: 0.2709 time to fit residues: 32.8481 Evaluate side-chains 68 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 338 LYS Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 414 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.5471 moved from start: 0.7518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16214 Z= 0.237 Angle : 0.687 14.985 24589 Z= 0.347 Chirality : 0.035 0.244 3165 Planarity : 0.005 0.065 1084 Dihedral : 25.358 165.833 8721 Min Nonbonded Distance : 0.904 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.67 % Favored : 96.06 % Rotamer: Outliers : 7.04 % Allowed : 29.91 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.42), residues: 381 helix: 0.49 (0.31), residues: 266 sheet: -0.62 (0.94), residues: 29 loop : -1.94 (0.59), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP D 328 HIS 0.003 0.001 HIS D 291 PHE 0.021 0.003 PHE D 298 TYR 0.018 0.003 TYR D 350 ARG 0.005 0.001 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 57 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.6653 (p90) REVERT: D 173 LYS cc_start: 0.6698 (mmtm) cc_final: 0.5420 (mttt) REVERT: D 310 TRP cc_start: 0.6958 (OUTLIER) cc_final: 0.6037 (t60) REVERT: D 323 GLN cc_start: 0.6050 (OUTLIER) cc_final: 0.3870 (tm-30) outliers start: 24 outliers final: 13 residues processed: 76 average time/residue: 0.2748 time to fit residues: 30.5570 Evaluate side-chains 67 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 51 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 ASN Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 338 LYS Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 414 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 overall best weight: 5.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5640 moved from start: 0.8972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16214 Z= 0.335 Angle : 0.817 12.885 24589 Z= 0.412 Chirality : 0.041 0.256 3165 Planarity : 0.006 0.080 1084 Dihedral : 25.724 168.412 8721 Min Nonbonded Distance : 1.044 Molprobity Statistics. All-atom Clashscore : 28.95 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.46 % Favored : 95.28 % Rotamer: Outliers : 7.04 % Allowed : 31.67 % Favored : 61.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.42), residues: 381 helix: 0.42 (0.31), residues: 262 sheet: -0.08 (0.92), residues: 24 loop : -2.15 (0.60), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.005 TRP D 328 HIS 0.007 0.002 HIS D 291 PHE 0.017 0.003 PHE D 221 TYR 0.025 0.003 TYR D 392 ARG 0.006 0.001 ARG D 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 55 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: D 155 MET cc_start: 0.7611 (mtt) cc_final: 0.6983 (mtt) REVERT: D 172 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7613 (ttm110) REVERT: D 173 LYS cc_start: 0.6943 (mmtm) cc_final: 0.5756 (mttt) REVERT: D 299 LYS cc_start: 0.6874 (mtpt) cc_final: 0.6553 (mttp) REVERT: D 310 TRP cc_start: 0.7034 (OUTLIER) cc_final: 0.6182 (t60) REVERT: D 323 GLN cc_start: 0.6285 (OUTLIER) cc_final: 0.4162 (tm-30) outliers start: 24 outliers final: 18 residues processed: 75 average time/residue: 0.2676 time to fit residues: 29.6504 Evaluate side-chains 70 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 50 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 ASN Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 414 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 52 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 overall best weight: 5.7788 ------------------------------------------------------------------------------- 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: 0.5628 moved from start: 0.9394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16214 Z= 0.332 Angle : 0.786 12.381 24589 Z= 0.397 Chirality : 0.040 0.225 3165 Planarity : 0.006 0.060 1084 Dihedral : 25.629 165.497 8721 Min Nonbonded Distance : 0.993 Molprobity Statistics. All-atom Clashscore : 27.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.46 % Favored : 95.28 % Rotamer: Outliers : 7.92 % Allowed : 33.14 % Favored : 58.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.42), residues: 381 helix: 0.41 (0.32), residues: 261 sheet: -0.27 (0.92), residues: 24 loop : -2.20 (0.59), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP D 328 HIS 0.004 0.001 HIS D 291 PHE 0.014 0.003 PHE D 146 TYR 0.023 0.003 TYR D 392 ARG 0.005 0.001 ARG D 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 52 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 173 LYS cc_start: 0.7069 (mmtm) cc_final: 0.5969 (mttt) REVERT: D 272 TYR cc_start: 0.6255 (OUTLIER) cc_final: 0.4859 (t80) REVERT: D 310 TRP cc_start: 0.6875 (OUTLIER) cc_final: 0.5926 (t60) REVERT: D 323 GLN cc_start: 0.6252 (OUTLIER) cc_final: 0.4185 (tm-30) outliers start: 27 outliers final: 16 residues processed: 72 average time/residue: 0.2931 time to fit residues: 30.8308 Evaluate side-chains 71 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 52 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 272 TYR Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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: 0.5594 moved from start: 0.9615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16214 Z= 0.280 Angle : 0.732 12.183 24589 Z= 0.372 Chirality : 0.038 0.218 3165 Planarity : 0.005 0.045 1084 Dihedral : 25.583 164.772 8721 Min Nonbonded Distance : 1.031 Molprobity Statistics. All-atom Clashscore : 24.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.46 % Favored : 95.28 % Rotamer: Outliers : 5.57 % Allowed : 32.84 % Favored : 61.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.42), residues: 381 helix: 0.68 (0.32), residues: 262 sheet: -0.12 (0.96), residues: 24 loop : -2.32 (0.59), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 328 HIS 0.004 0.001 HIS D 291 PHE 0.015 0.003 PHE D 113 TYR 0.018 0.003 TYR D 392 ARG 0.005 0.001 ARG D 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 53 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 173 LYS cc_start: 0.7119 (mmtm) cc_final: 0.5949 (mttt) REVERT: D 299 LYS cc_start: 0.7015 (mtpt) cc_final: 0.6580 (mttp) REVERT: D 310 TRP cc_start: 0.6795 (OUTLIER) cc_final: 0.5810 (t60) REVERT: D 323 GLN cc_start: 0.6196 (OUTLIER) cc_final: 0.4107 (tm-30) outliers start: 19 outliers final: 16 residues processed: 71 average time/residue: 0.2754 time to fit residues: 28.9716 Evaluate side-chains 68 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 50 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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: 0.5522 moved from start: 0.9680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16214 Z= 0.218 Angle : 0.679 12.331 24589 Z= 0.345 Chirality : 0.035 0.211 3165 Planarity : 0.005 0.045 1084 Dihedral : 25.458 163.141 8721 Min Nonbonded Distance : 1.069 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.72 % Favored : 95.01 % Rotamer: Outliers : 6.16 % Allowed : 32.55 % Favored : 61.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.43), residues: 381 helix: 0.90 (0.32), residues: 261 sheet: 0.06 (0.97), residues: 24 loop : -2.29 (0.60), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 328 HIS 0.003 0.001 HIS D 291 PHE 0.016 0.003 PHE D 113 TYR 0.016 0.002 TYR D 392 ARG 0.004 0.001 ARG D 377 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 50 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 173 LYS cc_start: 0.6931 (mmtm) cc_final: 0.5701 (mttt) REVERT: D 299 LYS cc_start: 0.6963 (mtpt) cc_final: 0.6539 (mttp) REVERT: D 310 TRP cc_start: 0.6617 (OUTLIER) cc_final: 0.5737 (t60) REVERT: D 323 GLN cc_start: 0.6122 (OUTLIER) cc_final: 0.4135 (tm-30) outliers start: 21 outliers final: 17 residues processed: 68 average time/residue: 0.2746 time to fit residues: 27.3345 Evaluate side-chains 67 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 48 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 414 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 chunk 87 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 overall best weight: 2.8146 ------------------------------------------------------------------------------- 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: 0.5496 moved from start: 0.9754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16214 Z= 0.200 Angle : 0.661 12.083 24589 Z= 0.336 Chirality : 0.034 0.209 3165 Planarity : 0.005 0.044 1084 Dihedral : 25.373 162.724 8721 Min Nonbonded Distance : 1.071 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.99 % Favored : 94.75 % Rotamer: Outliers : 5.28 % Allowed : 34.60 % Favored : 60.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.43), residues: 381 helix: 0.97 (0.32), residues: 262 sheet: 0.15 (0.97), residues: 24 loop : -2.10 (0.63), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 328 HIS 0.006 0.002 HIS D 151 PHE 0.017 0.002 PHE D 113 TYR 0.016 0.002 TYR D 350 ARG 0.004 0.001 ARG D 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 51 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6696 (p90) REVERT: D 173 LYS cc_start: 0.6911 (mmtm) cc_final: 0.5666 (mttt) REVERT: D 323 GLN cc_start: 0.6065 (OUTLIER) cc_final: 0.4089 (tm-30) REVERT: D 416 MET cc_start: 0.8096 (mmm) cc_final: 0.7702 (mmp) outliers start: 18 outliers final: 15 residues processed: 67 average time/residue: 0.2963 time to fit residues: 29.1333 Evaluate side-chains 66 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 49 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 414 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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: 0.5445 moved from start: 0.9815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16214 Z= 0.180 Angle : 0.632 12.460 24589 Z= 0.321 Chirality : 0.033 0.207 3165 Planarity : 0.004 0.041 1084 Dihedral : 25.230 161.514 8721 Min Nonbonded Distance : 1.088 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.77 % Favored : 93.96 % Rotamer: Outliers : 4.40 % Allowed : 34.60 % Favored : 61.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.43), residues: 381 helix: 1.11 (0.32), residues: 261 sheet: 0.03 (0.98), residues: 24 loop : -2.11 (0.63), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 328 HIS 0.003 0.001 HIS D 291 PHE 0.018 0.002 PHE D 113 TYR 0.016 0.002 TYR D 350 ARG 0.005 0.001 ARG D 377 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 52 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6741 (p90) REVERT: D 173 LYS cc_start: 0.7003 (mmtm) cc_final: 0.5733 (mttt) REVERT: D 310 TRP cc_start: 0.6549 (OUTLIER) cc_final: 0.5726 (t60) outliers start: 15 outliers final: 12 residues processed: 66 average time/residue: 0.2637 time to fit residues: 25.6731 Evaluate side-chains 65 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 33 ASP Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 221 PHE Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 414 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.0070 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 52 optimal weight: 30.0000 overall best weight: 6.6008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.068066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.054630 restraints weight = 110534.242| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.97 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 1.0282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16214 Z= 0.367 Angle : 0.824 12.527 24589 Z= 0.414 Chirality : 0.042 0.236 3165 Planarity : 0.006 0.062 1084 Dihedral : 25.685 166.850 8721 Min Nonbonded Distance : 0.996 Molprobity Statistics. All-atom Clashscore : 29.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.04 % Favored : 93.70 % Rotamer: Outliers : 5.57 % Allowed : 34.31 % Favored : 60.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.42), residues: 381 helix: 0.62 (0.32), residues: 260 sheet: -0.34 (1.05), residues: 14 loop : -2.12 (0.57), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 328 HIS 0.005 0.001 HIS D 291 PHE 0.017 0.003 PHE D 113 TYR 0.025 0.003 TYR D 392 ARG 0.007 0.001 ARG D 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2102.38 seconds wall clock time: 39 minutes 44.11 seconds (2384.11 seconds total)