Starting phenix.real_space_refine on Sun Sep 29 00:40:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/09_2024/6mec_9106.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/09_2024/6mec_9106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/09_2024/6mec_9106.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/09_2024/6mec_9106.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/09_2024/6mec_9106.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/09_2024/6mec_9106.cif" } resolution = 3.6 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= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians P 832 5.49 5 Mg 51 5.21 5 S 8 5.16 5 Na 1 4.78 5 C 10129 2.51 5 N 3918 2.21 5 O 6337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 21276 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 17537 Classifications: {'DNA': 1, 'RNA': 817} Modifications used: {'rna2p_pur': 53, 'rna2p_pyr': 34, 'rna3p_pur': 407, 'rna3p_pyr': 323} Link IDs: {'rna2p': 87, 'rna3p': 730} Chain breaks: 2 Chain: "B" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 294 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "C" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3393 Classifications: {'peptide': 414} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 398} Chain breaks: 2 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Unusual residues: {' MG': 50, ' NA': 1} Classifications: {'undetermined': 51} Link IDs: {None: 50} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.36, per 1000 atoms: 0.67 Number of scatterers: 21276 At special positions: 0 Unit cell: (116.13, 154.05, 237, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 8 16.00 P 832 15.00 Mg 51 11.99 Na 1 11.00 O 6337 8.00 N 3918 7.00 C 10129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.52 Conformation dependent library (CDL) restraints added in 942.4 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 776 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 3 sheets defined 53.4% alpha, 6.3% beta 279 base pairs and 440 stacking pairs defined. Time for finding SS restraints: 10.52 Creating SS restraints... Processing helix chain 'C' and resid 27 through 48 removed outlier: 4.384A pdb=" N ASN C 32 " --> pdb=" O TRP C 28 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ARG C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU C 48 " --> pdb=" O LYS C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 63 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 93 through 105 removed outlier: 4.176A pdb=" N LEU C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 154 Proline residue: C 149 - end of helix removed outlier: 3.567A pdb=" N THR C 153 " --> pdb=" O PRO C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 179 removed outlier: 3.535A pdb=" N ALA C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 212 through 222 Processing helix chain 'C' and resid 243 through 252 removed outlier: 3.752A pdb=" N LEU C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 285 through 300 removed outlier: 3.520A pdb=" N GLU C 300 " --> pdb=" O GLU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 356 Processing helix chain 'C' and resid 360 through 378 Proline residue: C 370 - end of helix Processing helix chain 'C' and resid 384 through 406 Processing helix chain 'C' and resid 411 through 420 Processing helix chain 'C' and resid 448 through 452 removed outlier: 3.837A pdb=" N THR C 452 " --> pdb=" O ALA C 449 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 115 through 119 removed outlier: 3.994A pdb=" N VAL C 117 " --> pdb=" O LEU C 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 270 through 273 removed outlier: 4.190A pdb=" N PHE C 277 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 191 " --> pdb=" O PHE C 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 319 through 321 163 hydrogen bonds defined for protein. 465 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 725 hydrogen bonds 1260 hydrogen bond angles 0 basepair planarities 279 basepair parallelities 440 stacking parallelities Total time for adding SS restraints: 14.39 Time building geometry restraints manager: 6.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2006 1.32 - 1.44: 11160 1.44 - 1.56: 8588 1.56 - 1.68: 1663 1.68 - 1.80: 12 Bond restraints: 23429 Sorted by residual: bond pdb=" N PRO C 132 " pdb=" CD PRO C 132 " ideal model delta sigma weight residual 1.473 1.416 0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" N PRO C 245 " pdb=" CD PRO C 245 " ideal model delta sigma weight residual 1.473 1.430 0.043 1.40e-02 5.10e+03 9.60e+00 bond pdb=" CB ASN C 389 " pdb=" CG ASN C 389 " ideal model delta sigma weight residual 1.516 1.446 0.070 2.50e-02 1.60e+03 7.74e+00 bond pdb=" CB ARG C 406 " pdb=" CG ARG C 406 " ideal model delta sigma weight residual 1.520 1.438 0.082 3.00e-02 1.11e+03 7.49e+00 bond pdb=" CE3 TRP C 402 " pdb=" CZ3 TRP C 402 " ideal model delta sigma weight residual 1.382 1.303 0.079 3.00e-02 1.11e+03 6.89e+00 ... (remaining 23424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 34100 2.49 - 4.99: 1454 4.99 - 7.48: 192 7.48 - 9.97: 37 9.97 - 12.47: 9 Bond angle restraints: 35792 Sorted by residual: angle pdb=" C3' A A 481 " pdb=" O3' A A 481 " pdb=" P U A 482 " ideal model delta sigma weight residual 120.20 128.24 -8.04 1.50e+00 4.44e-01 2.87e+01 angle pdb=" C3' U A 545 " pdb=" O3' U A 545 " pdb=" P C A 546 " ideal model delta sigma weight residual 120.20 127.78 -7.58 1.50e+00 4.44e-01 2.55e+01 angle pdb=" C3' A A 462 " pdb=" O3' A A 462 " pdb=" P U A 463 " ideal model delta sigma weight residual 120.20 127.58 -7.38 1.50e+00 4.44e-01 2.42e+01 angle pdb=" O3' A A 12 " pdb=" C3' A A 12 " pdb=" C2' A A 12 " ideal model delta sigma weight residual 113.70 120.85 -7.15 1.50e+00 4.44e-01 2.27e+01 angle pdb=" C3' C A 666 " pdb=" O3' C A 666 " pdb=" P A A 667 " ideal model delta sigma weight residual 120.20 127.31 -7.11 1.50e+00 4.44e-01 2.24e+01 ... (remaining 35787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 12656 35.58 - 71.16: 2052 71.16 - 106.74: 274 106.74 - 142.33: 8 142.33 - 177.91: 10 Dihedral angle restraints: 15000 sinusoidal: 13802 harmonic: 1198 Sorted by residual: dihedral pdb=" O4' U A 258 " pdb=" C1' U A 258 " pdb=" N1 U A 258 " pdb=" C2 U A 258 " ideal model delta sinusoidal sigma weight residual -128.00 49.91 -177.91 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U A 839 " pdb=" C1' U A 839 " pdb=" N1 U A 839 " pdb=" C2 U A 839 " ideal model delta sinusoidal sigma weight residual -128.00 45.05 -173.05 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" CA TYR C 273 " pdb=" C TYR C 273 " pdb=" N ALA C 274 " pdb=" CA ALA C 274 " ideal model delta harmonic sigma weight residual -180.00 -140.17 -39.83 0 5.00e+00 4.00e-02 6.35e+01 ... (remaining 14997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4117 0.088 - 0.175: 475 0.175 - 0.263: 40 0.263 - 0.351: 8 0.351 - 0.439: 4 Chirality restraints: 4644 Sorted by residual: chirality pdb=" C1' A A 401 " pdb=" O4' A A 401 " pdb=" C2' A A 401 " pdb=" N9 A A 401 " both_signs ideal model delta sigma weight residual False 2.44 2.00 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" C3' G A 8 " pdb=" C4' G A 8 " pdb=" O3' G A 8 " pdb=" C2' G A 8 " both_signs ideal model delta sigma weight residual False -2.48 -2.10 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C3' G A 832 " pdb=" C4' G A 832 " pdb=" O3' G A 832 " pdb=" C2' G A 832 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.40e+00 ... (remaining 4641 not shown) Planarity restraints: 1417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 238 " -0.049 2.00e-02 2.50e+03 2.15e-02 1.27e+01 pdb=" N9 A A 238 " 0.047 2.00e-02 2.50e+03 pdb=" C8 A A 238 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A A 238 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A 238 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A A 238 " -0.008 2.00e-02 2.50e+03 pdb=" N6 A A 238 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A A 238 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A A 238 " 0.005 2.00e-02 2.50e+03 pdb=" N3 A A 238 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A A 238 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 407 " 0.057 5.00e-02 4.00e+02 8.68e-02 1.20e+01 pdb=" N PRO C 408 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 408 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 408 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A A 401 " 0.044 2.00e-02 2.50e+03 1.84e-02 9.34e+00 pdb=" N9 A A 401 " -0.035 2.00e-02 2.50e+03 pdb=" C8 A A 401 " -0.007 2.00e-02 2.50e+03 pdb=" N7 A A 401 " -0.005 2.00e-02 2.50e+03 pdb=" C5 A A 401 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A A 401 " 0.010 2.00e-02 2.50e+03 pdb=" N6 A A 401 " 0.011 2.00e-02 2.50e+03 pdb=" N1 A A 401 " 0.008 2.00e-02 2.50e+03 pdb=" C2 A A 401 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A A 401 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A A 401 " -0.015 2.00e-02 2.50e+03 ... (remaining 1414 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 75 2.31 - 2.96: 9335 2.96 - 3.60: 36914 3.60 - 4.25: 64238 4.25 - 4.90: 82886 Nonbonded interactions: 193448 Sorted by model distance: nonbonded pdb=" CZ2 TRP C 28 " pdb=" CD LYS C 73 " model vdw 1.659 3.740 nonbonded pdb=" NE ARG C 380 " pdb=" OE1 GLN C 455 " model vdw 1.667 3.120 nonbonded pdb=" P U A 1 " pdb=" O2' A A 860 " model vdw 1.676 3.400 nonbonded pdb=" O LEU C 356 " pdb=" CH2 TRP C 402 " model vdw 1.793 3.340 nonbonded pdb=" O2' A A 428 " pdb=" OP1 A A 429 " model vdw 1.851 3.040 ... (remaining 193443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.130 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: 0.030 Extract box with map and model: 0.980 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 61.630 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 : 0.010 0.099 23429 Z= 0.612 Angle : 1.213 12.467 35792 Z= 0.589 Chirality : 0.058 0.439 4644 Planarity : 0.008 0.087 1417 Dihedral : 25.555 177.907 14224 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.73 % Favored : 86.27 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -4.93 (0.32), residues: 408 helix: -3.26 (0.23), residues: 212 sheet: -1.60 (0.94), residues: 34 loop : -3.49 (0.42), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.006 TRP C 324 HIS 0.018 0.006 HIS C 346 PHE 0.051 0.006 PHE C 231 TYR 0.035 0.004 TYR C 378 ARG 0.009 0.002 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: C 231 PHE cc_start: 0.8259 (p90) cc_final: 0.7870 (p90) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.4503 time to fit residues: 65.2292 Evaluate side-chains 48 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN C 202 HIS C 269 ASN C 341 ASN C 346 HIS ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 HIS C 417 ASN C 455 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23429 Z= 0.238 Angle : 0.716 8.889 35792 Z= 0.360 Chirality : 0.037 0.274 4644 Planarity : 0.006 0.051 1417 Dihedral : 25.968 179.698 13361 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 2.82 % Allowed : 10.14 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.38), residues: 408 helix: -1.47 (0.32), residues: 216 sheet: -1.58 (0.84), residues: 34 loop : -3.17 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP C 396 HIS 0.008 0.002 HIS C 346 PHE 0.031 0.003 PHE C 231 TYR 0.020 0.003 TYR C 66 ARG 0.008 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.965 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 70 average time/residue: 0.4686 time to fit residues: 48.1118 Evaluate side-chains 59 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 379 HIS Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 433 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 341 ASN ** C 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23429 Z= 0.165 Angle : 0.628 8.032 35792 Z= 0.315 Chirality : 0.032 0.265 4644 Planarity : 0.005 0.046 1417 Dihedral : 25.676 178.047 13361 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 3.66 % Allowed : 13.24 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.41), residues: 408 helix: -0.36 (0.34), residues: 217 sheet: -1.26 (0.79), residues: 34 loop : -3.01 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 396 HIS 0.004 0.001 HIS C 397 PHE 0.020 0.002 PHE C 231 TYR 0.010 0.002 TYR C 109 ARG 0.009 0.001 ARG C 413 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.941 Fit side-chains REVERT: C 405 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8315 (ttt-90) outliers start: 13 outliers final: 5 residues processed: 73 average time/residue: 0.4174 time to fit residues: 44.0689 Evaluate side-chains 55 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 433 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 0.0020 chunk 118 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.8592 ------------------------------------------------------------------------------- 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: 0.7704 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23429 Z= 0.237 Angle : 0.662 8.901 35792 Z= 0.331 Chirality : 0.034 0.269 4644 Planarity : 0.005 0.039 1417 Dihedral : 25.648 179.756 13361 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 4.23 % Allowed : 14.65 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.88 (0.42), residues: 408 helix: -0.07 (0.35), residues: 214 sheet: -0.78 (0.85), residues: 32 loop : -3.04 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 402 HIS 0.007 0.002 HIS C 346 PHE 0.016 0.002 PHE C 231 TYR 0.019 0.002 TYR C 109 ARG 0.006 0.001 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 47 time to evaluate : 0.903 Fit side-chains REVERT: C 246 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7696 (mtt) REVERT: C 379 HIS cc_start: 0.8775 (OUTLIER) cc_final: 0.8534 (p-80) outliers start: 15 outliers final: 6 residues processed: 58 average time/residue: 0.3535 time to fit residues: 31.5251 Evaluate side-chains 54 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 379 HIS Chi-restraints excluded: chain C residue 433 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 88 optimal weight: 0.1980 chunk 49 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 GLN C 266 GLN C 269 ASN C 346 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23429 Z= 0.270 Angle : 0.680 9.026 35792 Z= 0.340 Chirality : 0.034 0.270 4644 Planarity : 0.005 0.044 1417 Dihedral : 25.646 178.847 13361 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 4.79 % Allowed : 15.49 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.71 (0.42), residues: 408 helix: 0.07 (0.35), residues: 214 sheet: -0.71 (0.89), residues: 30 loop : -2.91 (0.51), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 402 HIS 0.008 0.002 HIS C 346 PHE 0.025 0.002 PHE C 231 TYR 0.015 0.002 TYR C 109 ARG 0.005 0.001 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 0.938 Fit side-chains REVERT: C 70 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8108 (mm) REVERT: C 246 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7662 (mtt) outliers start: 17 outliers final: 10 residues processed: 60 average time/residue: 0.3668 time to fit residues: 33.9856 Evaluate side-chains 55 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 43 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 433 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 23429 Z= 0.320 Angle : 0.728 8.140 35792 Z= 0.363 Chirality : 0.037 0.274 4644 Planarity : 0.005 0.049 1417 Dihedral : 25.697 178.999 13361 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 4.79 % Allowed : 19.15 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.88 (0.42), residues: 408 helix: 0.00 (0.35), residues: 214 sheet: -0.95 (0.85), residues: 30 loop : -3.08 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 402 HIS 0.007 0.002 HIS C 346 PHE 0.012 0.002 PHE C 197 TYR 0.012 0.002 TYR C 109 ARG 0.005 0.001 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 0.929 Fit side-chains REVERT: C 70 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8233 (mm) REVERT: C 246 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7846 (mtt) outliers start: 17 outliers final: 13 residues processed: 60 average time/residue: 0.3644 time to fit residues: 33.7824 Evaluate side-chains 56 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 433 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 chunk 118 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 379 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 23429 Z= 0.303 Angle : 0.710 7.926 35792 Z= 0.355 Chirality : 0.036 0.274 4644 Planarity : 0.005 0.049 1417 Dihedral : 25.683 178.997 13361 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 5.35 % Allowed : 19.15 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.84 (0.42), residues: 408 helix: 0.02 (0.35), residues: 214 sheet: -0.75 (0.91), residues: 30 loop : -3.08 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 402 HIS 0.008 0.002 HIS C 346 PHE 0.012 0.002 PHE C 231 TYR 0.014 0.002 TYR C 143 ARG 0.004 0.001 ARG C 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 43 time to evaluate : 0.992 Fit side-chains REVERT: C 70 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8211 (mm) REVERT: C 192 ASP cc_start: 0.6974 (m-30) cc_final: 0.6546 (m-30) REVERT: C 246 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7808 (mtt) outliers start: 19 outliers final: 14 residues processed: 57 average time/residue: 0.3779 time to fit residues: 32.6664 Evaluate side-chains 56 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 40 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 226 TRP Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 433 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 23429 Z= 0.310 Angle : 0.714 7.978 35792 Z= 0.357 Chirality : 0.036 0.274 4644 Planarity : 0.005 0.049 1417 Dihedral : 25.676 178.976 13361 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 5.35 % Allowed : 18.87 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.87 (0.42), residues: 408 helix: 0.01 (0.35), residues: 214 sheet: -0.84 (0.90), residues: 30 loop : -3.09 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 59 HIS 0.008 0.003 HIS C 346 PHE 0.011 0.002 PHE C 231 TYR 0.016 0.002 TYR C 143 ARG 0.004 0.001 ARG C 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 41 time to evaluate : 1.009 Fit side-chains REVERT: C 70 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8218 (mm) REVERT: C 192 ASP cc_start: 0.6743 (m-30) cc_final: 0.6494 (m-30) REVERT: C 246 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7844 (mtt) outliers start: 19 outliers final: 16 residues processed: 55 average time/residue: 0.3740 time to fit residues: 31.9321 Evaluate side-chains 58 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 40 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 226 TRP Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 433 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.4980 chunk 110 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 66 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 116 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7570 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23429 Z= 0.143 Angle : 0.586 6.459 35792 Z= 0.293 Chirality : 0.030 0.257 4644 Planarity : 0.004 0.035 1417 Dihedral : 25.408 177.815 13361 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.82 % Allowed : 21.69 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.50 (0.42), residues: 408 helix: 0.52 (0.35), residues: 220 sheet: -1.43 (1.07), residues: 24 loop : -3.17 (0.44), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 59 HIS 0.004 0.001 HIS C 314 PHE 0.017 0.002 PHE C 231 TYR 0.012 0.002 TYR C 143 ARG 0.005 0.001 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: C 139 MET cc_start: 0.6821 (mmp) cc_final: 0.6329 (mmp) REVERT: C 192 ASP cc_start: 0.6757 (m-30) cc_final: 0.6469 (m-30) REVERT: C 396 TRP cc_start: 0.8370 (t60) cc_final: 0.7897 (t60) outliers start: 10 outliers final: 6 residues processed: 56 average time/residue: 0.3776 time to fit residues: 32.2120 Evaluate side-chains 52 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 433 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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: 0.7755 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 23429 Z= 0.321 Angle : 0.708 7.843 35792 Z= 0.354 Chirality : 0.036 0.262 4644 Planarity : 0.005 0.045 1417 Dihedral : 25.552 179.267 13361 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 1.69 % Allowed : 23.10 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.83 (0.41), residues: 408 helix: 0.30 (0.35), residues: 215 sheet: -0.92 (0.86), residues: 32 loop : -3.50 (0.43), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 59 HIS 0.008 0.002 HIS C 397 PHE 0.015 0.002 PHE C 321 TYR 0.013 0.002 TYR C 143 ARG 0.004 0.001 ARG C 380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: C 192 ASP cc_start: 0.6907 (m-30) cc_final: 0.6694 (m-30) outliers start: 6 outliers final: 6 residues processed: 48 average time/residue: 0.3910 time to fit residues: 27.8644 Evaluate side-chains 49 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 433 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 100 optimal weight: 0.0870 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 overall best weight: 2.4166 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.120905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.092394 restraints weight = 57540.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.093692 restraints weight = 34980.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.093654 restraints weight = 24636.678| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 23429 Z= 0.287 Angle : 0.685 7.767 35792 Z= 0.343 Chirality : 0.035 0.267 4644 Planarity : 0.005 0.053 1417 Dihedral : 25.545 179.118 13361 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 2.25 % Allowed : 22.54 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % 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: -1.93 (0.40), residues: 408 helix: 0.21 (0.35), residues: 215 sheet: -0.99 (0.85), residues: 32 loop : -3.54 (0.43), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 59 HIS 0.006 0.002 HIS C 397 PHE 0.021 0.002 PHE C 162 TYR 0.017 0.002 TYR C 143 ARG 0.004 0.001 ARG C 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2436.18 seconds wall clock time: 50 minutes 58.27 seconds (3058.27 seconds total)