Starting phenix.real_space_refine on Mon Mar 18 14:19:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/03_2024/6mec_9106.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/03_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_9106/03_2024/6mec_9106.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/03_2024/6mec_9106.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/03_2024/6mec_9106.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mec_9106/03_2024/6mec_9106.pdb" } 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 Residue "C ARG 413": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 11.53, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.62 Conformation dependent library (CDL) restraints added in 699.7 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: 10.28 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: 14.14 Time building geometry restraints manager: 13.36 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: 94.17 - 102.87: 1653 102.87 - 111.56: 14206 111.56 - 120.26: 11824 120.26 - 128.95: 7268 128.95 - 137.65: 841 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 2.520 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 2.440 ... (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 ========== 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: 4.240 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: 0.020 Extract box with map and model: 14.510 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 70.090 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.660 ------------------------------------------------------------------------------- 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 : 0.921 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: 0.4720 time to fit residues: 68.6090 Evaluate side-chains 48 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.9980 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23429 Z= 0.217 Angle : 0.689 8.779 35792 Z= 0.347 Chirality : 0.035 0.281 4644 Planarity : 0.005 0.053 1417 Dihedral : 25.969 179.915 13361 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.38 % Allowed : 9.58 % 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: -3.28 (0.37), residues: 408 helix: -1.51 (0.31), residues: 216 sheet: -1.48 (0.85), residues: 34 loop : -3.21 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP C 396 HIS 0.008 0.002 HIS C 346 PHE 0.030 0.002 PHE C 231 TYR 0.016 0.002 TYR C 109 ARG 0.007 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 82 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.765 Fit side-chains REVERT: C 204 TRP cc_start: 0.7955 (t60) cc_final: 0.7738 (t60) REVERT: C 231 PHE cc_start: 0.8202 (p90) cc_final: 0.7782 (p90) REVERT: C 275 ASP cc_start: 0.7705 (p0) cc_final: 0.7495 (p0) REVERT: C 379 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.8288 (p-80) outliers start: 12 outliers final: 7 residues processed: 77 average time/residue: 0.4036 time to fit residues: 44.3374 Evaluate side-chains 60 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 147 LEU Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 379 HIS 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: 3.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 99 optimal weight: 0.0570 chunk 110 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.1700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN C 341 ASN ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23429 Z= 0.175 Angle : 0.620 9.156 35792 Z= 0.310 Chirality : 0.032 0.269 4644 Planarity : 0.005 0.047 1417 Dihedral : 25.707 179.125 13361 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 3.66 % Allowed : 12.96 % Favored : 83.38 % 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: -2.25 (0.40), residues: 408 helix: -0.38 (0.34), residues: 217 sheet: -1.19 (0.81), residues: 34 loop : -3.19 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 396 HIS 0.005 0.001 HIS C 397 PHE 0.020 0.002 PHE C 231 TYR 0.011 0.002 TYR C 187 ARG 0.006 0.001 ARG C 33 *********************** 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 70 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.952 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 64 average time/residue: 0.4241 time to fit residues: 39.2153 Evaluate side-chains 54 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 184 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 304 THR 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: 2.9990 chunk 58 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23429 Z= 0.252 Angle : 0.662 8.843 35792 Z= 0.331 Chirality : 0.034 0.274 4644 Planarity : 0.005 0.039 1417 Dihedral : 25.702 179.308 13361 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 4.23 % Allowed : 14.93 % Favored : 80.85 % 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 (0.41), residues: 408 helix: -0.14 (0.34), residues: 217 sheet: -0.49 (0.89), residues: 32 loop : -3.11 (0.48), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 396 HIS 0.007 0.002 HIS C 346 PHE 0.015 0.002 PHE C 231 TYR 0.013 0.002 TYR C 329 ARG 0.004 0.001 ARG C 37 *********************** 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 64 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: C 379 HIS cc_start: 0.8843 (OUTLIER) cc_final: 0.8526 (p-80) outliers start: 15 outliers final: 11 residues processed: 61 average time/residue: 0.3712 time to fit residues: 34.3621 Evaluate side-chains 59 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 114 LEU 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 211 LEU Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 304 THR 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: 5.9990 chunk 49 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 GLN C 269 ASN C 346 HIS ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 23429 Z= 0.414 Angle : 0.813 9.173 35792 Z= 0.404 Chirality : 0.041 0.287 4644 Planarity : 0.006 0.056 1417 Dihedral : 25.872 179.517 13361 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.78 % Favored : 88.97 % Rotamer: Outliers : 6.20 % Allowed : 15.49 % Favored : 78.31 % 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: -2.34 (0.40), residues: 408 helix: -0.47 (0.34), residues: 215 sheet: -0.40 (0.93), residues: 32 loop : -3.36 (0.45), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 402 HIS 0.009 0.003 HIS C 346 PHE 0.024 0.003 PHE C 231 TYR 0.014 0.003 TYR C 143 ARG 0.006 0.001 ARG C 405 *********************** 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 69 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 47 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: C 70 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8395 (mm) REVERT: C 246 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7852 (mtm) outliers start: 22 outliers final: 16 residues processed: 64 average time/residue: 0.3888 time to fit residues: 37.5259 Evaluate side-chains 58 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 40 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 70 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 133 THR 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 211 LEU Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 379 HIS 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: 0.0370 chunk 23 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23429 Z= 0.247 Angle : 0.670 8.486 35792 Z= 0.334 Chirality : 0.034 0.279 4644 Planarity : 0.005 0.048 1417 Dihedral : 25.721 179.470 13361 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 6.20 % Allowed : 19.15 % Favored : 74.65 % 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 (0.41), residues: 408 helix: -0.02 (0.35), residues: 215 sheet: -0.50 (0.89), residues: 32 loop : -3.29 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 402 HIS 0.006 0.002 HIS C 346 PHE 0.023 0.002 PHE C 231 TYR 0.012 0.002 TYR C 143 ARG 0.004 0.001 ARG C 406 *********************** 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 67 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 45 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 70 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8219 (mm) REVERT: C 246 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7879 (mtm) outliers start: 22 outliers final: 15 residues processed: 62 average time/residue: 0.3637 time to fit residues: 34.3037 Evaluate side-chains 62 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 45 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 70 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 114 LEU 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 211 LEU Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 379 HIS 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: 4.9990 chunk 67 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 chunk 118 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 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 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 23429 Z= 0.317 Angle : 0.716 8.370 35792 Z= 0.357 Chirality : 0.036 0.278 4644 Planarity : 0.005 0.050 1417 Dihedral : 25.742 179.952 13361 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 6.20 % Allowed : 19.44 % Favored : 74.37 % 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: -1.95 (0.41), residues: 408 helix: -0.02 (0.35), residues: 215 sheet: -0.32 (0.93), residues: 32 loop : -3.38 (0.46), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 402 HIS 0.007 0.002 HIS C 397 PHE 0.010 0.002 PHE C 231 TYR 0.015 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 68 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 46 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 59 TRP cc_start: 0.8537 (t-100) cc_final: 0.7597 (t-100) REVERT: C 70 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8286 (mm) REVERT: C 246 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7923 (mtm) outliers start: 22 outliers final: 17 residues processed: 63 average time/residue: 0.3565 time to fit residues: 34.4054 Evaluate side-chains 63 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 44 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 70 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 379 HIS 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: 8.9990 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 113 optimal weight: 0.3980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 262 HIS ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 23429 Z= 0.291 Angle : 0.695 8.413 35792 Z= 0.347 Chirality : 0.035 0.277 4644 Planarity : 0.005 0.049 1417 Dihedral : 25.729 179.976 13361 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 6.76 % Allowed : 19.15 % Favored : 74.08 % 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: -1.95 (0.41), residues: 408 helix: 0.05 (0.34), residues: 215 sheet: -0.40 (0.94), residues: 32 loop : -3.47 (0.46), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 402 HIS 0.007 0.002 HIS C 346 PHE 0.011 0.002 PHE C 231 TYR 0.015 0.002 TYR C 143 ARG 0.005 0.001 ARG C 406 *********************** 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 69 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 45 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 70 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8265 (mm) REVERT: C 246 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7887 (mtm) outliers start: 24 outliers final: 19 residues processed: 64 average time/residue: 0.3469 time to fit residues: 34.1674 Evaluate side-chains 65 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 44 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 70 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 114 LEU 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 211 LEU Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 379 HIS 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: 0.0870 chunk 110 optimal weight: 0.7980 chunk 113 optimal weight: 0.3980 chunk 66 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 72 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23429 Z= 0.141 Angle : 0.581 7.342 35792 Z= 0.289 Chirality : 0.030 0.293 4644 Planarity : 0.004 0.031 1417 Dihedral : 25.444 179.583 13361 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 3.66 % Allowed : 21.97 % Favored : 74.37 % 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: -1.38 (0.42), residues: 408 helix: 0.68 (0.35), residues: 220 sheet: -0.70 (0.88), residues: 32 loop : -3.46 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 59 HIS 0.004 0.001 HIS C 346 PHE 0.015 0.002 PHE C 345 TYR 0.013 0.001 TYR C 143 ARG 0.004 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 66 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 157 ARG cc_start: 0.7038 (mmm160) cc_final: 0.6536 (mtp85) REVERT: C 432 THR cc_start: 0.8418 (p) cc_final: 0.8177 (t) outliers start: 13 outliers final: 9 residues processed: 64 average time/residue: 0.3666 time to fit residues: 35.3940 Evaluate side-chains 57 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 184 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 310 THR 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: 0.9990 chunk 112 optimal weight: 0.5980 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: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 379 HIS ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23429 Z= 0.239 Angle : 0.636 7.428 35792 Z= 0.318 Chirality : 0.032 0.258 4644 Planarity : 0.005 0.041 1417 Dihedral : 25.482 179.414 13361 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 2.54 % Allowed : 23.94 % Favored : 73.52 % 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: -1.77 (0.40), residues: 408 helix: 0.38 (0.34), residues: 220 sheet: -0.93 (0.83), residues: 32 loop : -3.65 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 59 HIS 0.007 0.002 HIS C 397 PHE 0.009 0.002 PHE C 197 TYR 0.011 0.002 TYR C 143 ARG 0.004 0.001 ARG C 405 ********************** 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 57 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 192 ASP cc_start: 0.6522 (m-30) cc_final: 0.6168 (m-30) outliers start: 9 outliers final: 8 residues processed: 57 average time/residue: 0.3614 time to fit residues: 31.2824 Evaluate side-chains 54 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 184 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 310 THR 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: 0.5980 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.121383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.093267 restraints weight = 57663.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.094462 restraints weight = 36309.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.094608 restraints weight = 23904.432| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23429 Z= 0.265 Angle : 0.654 7.676 35792 Z= 0.327 Chirality : 0.033 0.266 4644 Planarity : 0.005 0.043 1417 Dihedral : 25.545 179.673 13361 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 3.10 % Allowed : 23.38 % Favored : 73.52 % 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: -1.99 (0.40), residues: 408 helix: 0.19 (0.34), residues: 220 sheet: -1.17 (0.84), residues: 32 loop : -3.70 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 59 HIS 0.006 0.002 HIS C 346 PHE 0.009 0.002 PHE C 197 TYR 0.014 0.002 TYR C 143 ARG 0.003 0.001 ARG C 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2413.27 seconds wall clock time: 46 minutes 21.98 seconds (2781.98 seconds total)