Starting phenix.real_space_refine on Sun Sep 29 02:59:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6me0_9105/09_2024/6me0_9105.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6me0_9105/09_2024/6me0_9105.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/6me0_9105/09_2024/6me0_9105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6me0_9105/09_2024/6me0_9105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6me0_9105/09_2024/6me0_9105.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6me0_9105/09_2024/6me0_9105.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 845 5.49 5 Mg 32 5.21 5 S 8 5.16 5 Na 1 4.78 5 C 10256 2.51 5 N 3976 2.21 5 O 6421 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: 21539 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 17776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 829, 17776 Classifications: {'RNA': 829} Modifications used: {'rna2p_pur': 55, 'rna2p_pyr': 33, 'rna3p_pur': 414, 'rna3p_pyr': 327} Link IDs: {'rna2p': 88, 'rna3p': 740} Chain breaks: 1 Chain: "B" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 337 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Unusual residues: {' MG': 32, ' NA': 1} Classifications: {'undetermined': 33} Link IDs: {None: 32} Time building chain proxies: 13.93, per 1000 atoms: 0.65 Number of scatterers: 21539 At special positions: 0 Unit cell: (111.39, 160.37, 233.05, 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 845 15.00 Mg 32 11.99 Na 1 11.00 O 6421 8.00 N 3976 7.00 C 10256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.93 Conformation dependent library (CDL) restraints added in 840.4 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 4 sheets defined 54.1% alpha, 7.2% beta 291 base pairs and 472 stacking pairs defined. Time for finding SS restraints: 10.80 Creating SS restraints... Processing helix chain 'C' and resid 27 through 47 removed outlier: 3.791A pdb=" N ASN C 32 " --> pdb=" O TRP C 28 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ARG C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 35 " --> pdb=" O ALA C 31 " (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: 3.702A 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: 3.768A pdb=" N THR C 153 " --> pdb=" O PRO C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 179 Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 212 through 222 removed outlier: 3.534A pdb=" N SER C 222 " --> pdb=" O LYS C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 251 Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 285 through 301 removed outlier: 3.750A pdb=" N GLU C 300 " --> pdb=" O GLU C 296 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG C 301 " --> pdb=" O PHE C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 356 removed outlier: 3.661A pdb=" N LYS C 343 " --> pdb=" O LYS C 339 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE C 345 " --> pdb=" O ASN C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 379 Proline residue: C 370 - end of helix removed outlier: 3.880A pdb=" N HIS C 379 " --> pdb=" O TRP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 407 removed outlier: 3.898A pdb=" N HIS C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 419 removed outlier: 3.805A pdb=" N THR C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 452 Processing sheet with id=AA1, first strand: chain 'C' and resid 115 through 119 removed outlier: 3.621A pdb=" N VAL C 117 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 119 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 270 through 273 Processing sheet with id=AA3, first strand: chain 'C' and resid 319 through 321 Processing sheet with id=AA4, first strand: chain 'C' and resid 420 through 421 165 hydrogen bonds defined for protein. 462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 755 hydrogen bonds 1294 hydrogen bond angles 0 basepair planarities 291 basepair parallelities 472 stacking parallelities Total time for adding SS restraints: 14.70 Time building geometry restraints manager: 5.92 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: 2097 1.32 - 1.44: 11238 1.44 - 1.56: 8713 1.56 - 1.67: 1688 1.67 - 1.79: 12 Bond restraints: 23748 Sorted by residual: bond pdb=" O3' U A 1 " pdb=" P U A 2 " ideal model delta sigma weight residual 1.607 1.460 0.147 1.50e-02 4.44e+03 9.66e+01 bond pdb=" CA HIS C 379 " pdb=" CB HIS C 379 " ideal model delta sigma weight residual 1.526 1.444 0.082 1.76e-02 3.23e+03 2.19e+01 bond pdb=" N PRO C 149 " pdb=" CD PRO C 149 " ideal model delta sigma weight residual 1.473 1.430 0.043 1.40e-02 5.10e+03 9.38e+00 bond pdb=" N PRO C 113 " pdb=" CD PRO C 113 " ideal model delta sigma weight residual 1.473 1.430 0.043 1.40e-02 5.10e+03 9.35e+00 bond pdb=" N PRO C 132 " pdb=" CD PRO C 132 " ideal model delta sigma weight residual 1.473 1.432 0.041 1.40e-02 5.10e+03 8.70e+00 ... (remaining 23743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 34957 2.61 - 5.22: 1169 5.22 - 7.83: 142 7.83 - 10.44: 18 10.44 - 13.04: 6 Bond angle restraints: 36292 Sorted by residual: angle pdb=" N ILE C 89 " pdb=" CA ILE C 89 " pdb=" C ILE C 89 " ideal model delta sigma weight residual 112.12 106.27 5.85 8.40e-01 1.42e+00 4.84e+01 angle pdb=" C GLN C 228 " pdb=" N GLN C 229 " pdb=" CA GLN C 229 " ideal model delta sigma weight residual 121.94 132.47 -10.53 1.76e+00 3.23e-01 3.58e+01 angle pdb=" N GLU C 317 " pdb=" CA GLU C 317 " pdb=" C GLU C 317 " ideal model delta sigma weight residual 114.39 106.14 8.25 1.45e+00 4.76e-01 3.24e+01 angle pdb=" C3' U A 477 " pdb=" O3' U A 477 " pdb=" P G A 478 " ideal model delta sigma weight residual 120.20 128.07 -7.87 1.50e+00 4.44e-01 2.75e+01 angle pdb=" C LYS C 416 " pdb=" N ASN C 417 " pdb=" CA ASN C 417 " ideal model delta sigma weight residual 122.54 114.15 8.39 1.65e+00 3.67e-01 2.59e+01 ... (remaining 36287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 12912 35.90 - 71.81: 2006 71.81 - 107.71: 257 107.71 - 143.61: 8 143.61 - 179.52: 8 Dihedral angle restraints: 15191 sinusoidal: 13993 harmonic: 1198 Sorted by residual: 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 -135.23 -44.77 0 5.00e+00 4.00e-02 8.02e+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 200.00 52.75 147.25 1 1.50e+01 4.44e-03 7.86e+01 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 232.00 52.48 179.52 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 15188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3998 0.074 - 0.147: 626 0.147 - 0.221: 69 0.221 - 0.294: 10 0.294 - 0.368: 5 Chirality restraints: 4708 Sorted by residual: 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 3.38e+00 chirality pdb=" C3' U A 764 " pdb=" C4' U A 764 " pdb=" O3' U A 764 " pdb=" C2' U A 764 " both_signs ideal model delta sigma weight residual False -2.48 -2.12 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C3' U A 545 " pdb=" C4' U A 545 " pdb=" O3' U A 545 " pdb=" C2' U A 545 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 4705 not shown) Planarity restraints: 1430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 56 " -0.011 2.00e-02 2.50e+03 2.73e-02 2.24e+01 pdb=" N9 G A 56 " 0.004 2.00e-02 2.50e+03 pdb=" C8 G A 56 " 0.007 2.00e-02 2.50e+03 pdb=" N7 G A 56 " -0.008 2.00e-02 2.50e+03 pdb=" C5 G A 56 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G A 56 " 0.023 2.00e-02 2.50e+03 pdb=" O6 G A 56 " -0.021 2.00e-02 2.50e+03 pdb=" N1 G A 56 " -0.009 2.00e-02 2.50e+03 pdb=" C2 G A 56 " 0.075 2.00e-02 2.50e+03 pdb=" N2 G A 56 " -0.045 2.00e-02 2.50e+03 pdb=" N3 G A 56 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G A 56 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 113 " -0.044 2.00e-02 2.50e+03 1.93e-02 1.12e+01 pdb=" N9 G A 113 " 0.042 2.00e-02 2.50e+03 pdb=" C8 G A 113 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G A 113 " 0.006 2.00e-02 2.50e+03 pdb=" C5 G A 113 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A 113 " -0.020 2.00e-02 2.50e+03 pdb=" O6 G A 113 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G A 113 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G A 113 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G A 113 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A 113 " 0.016 2.00e-02 2.50e+03 pdb=" C4 G A 113 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 262 " 0.043 2.00e-02 2.50e+03 1.84e-02 9.28e+00 pdb=" N9 A A 262 " -0.031 2.00e-02 2.50e+03 pdb=" C8 A A 262 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A A 262 " -0.008 2.00e-02 2.50e+03 pdb=" C5 A A 262 " -0.007 2.00e-02 2.50e+03 pdb=" C6 A A 262 " 0.000 2.00e-02 2.50e+03 pdb=" N6 A A 262 " 0.024 2.00e-02 2.50e+03 pdb=" N1 A A 262 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A A 262 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A A 262 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A A 262 " -0.008 2.00e-02 2.50e+03 ... (remaining 1427 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 32 2.20 - 2.88: 7351 2.88 - 3.55: 34573 3.55 - 4.23: 69641 4.23 - 4.90: 86898 Nonbonded interactions: 198495 Sorted by model distance: nonbonded pdb=" P U A 1 " pdb=" O2' A A 860 " model vdw 1.531 3.400 nonbonded pdb=" O LEU C 356 " pdb=" CH2 TRP C 402 " model vdw 1.616 3.340 nonbonded pdb=" CZ2 TRP C 28 " pdb=" CD LYS C 73 " model vdw 1.671 3.740 nonbonded pdb=" OD1 ASP C 366 " pdb=" NH2 ARG C 444 " model vdw 1.693 3.120 nonbonded pdb=" O2 U A 1 " pdb=" N1 G A 865 " model vdw 1.696 3.120 ... (remaining 198490 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: 7.880 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: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 60.500 Find NCS groups from input model: 0.130 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 0.147 23748 Z= 0.572 Angle : 1.156 13.045 36292 Z= 0.564 Chirality : 0.055 0.368 4708 Planarity : 0.007 0.070 1430 Dihedral : 25.122 179.517 14415 Min Nonbonded Distance : 1.531 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % 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 : 1.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.11 (0.30), residues: 408 helix: -2.85 (0.24), residues: 212 sheet: -2.47 (0.72), residues: 36 loop : -4.27 (0.38), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.005 TRP C 204 HIS 0.016 0.004 HIS C 346 PHE 0.039 0.005 PHE C 231 TYR 0.035 0.004 TYR C 378 ARG 0.012 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 95 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 LYS cc_start: 0.7923 (ptpt) cc_final: 0.7721 (ptpt) REVERT: C 118 TYR cc_start: 0.8201 (m-80) cc_final: 0.7975 (m-80) REVERT: C 276 ASP cc_start: 0.7764 (m-30) cc_final: 0.7359 (m-30) REVERT: C 429 VAL cc_start: 0.9186 (t) cc_final: 0.8924 (p) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.5518 time to fit residues: 70.1344 Evaluate side-chains 52 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 112 optimal weight: 0.5980 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 HIS C 269 ASN C 314 HIS C 346 HIS C 369 ASN C 377 ASN C 407 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23748 Z= 0.320 Angle : 0.753 8.962 36292 Z= 0.380 Chirality : 0.038 0.263 4708 Planarity : 0.005 0.044 1430 Dihedral : 25.555 177.478 13552 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 2.82 % Allowed : 6.20 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.81 (0.35), residues: 408 helix: -1.29 (0.31), residues: 216 sheet: -2.39 (0.76), residues: 36 loop : -4.40 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C 396 HIS 0.011 0.002 HIS C 346 PHE 0.034 0.004 PHE C 231 TYR 0.021 0.003 TYR C 378 ARG 0.004 0.001 ARG C 426 *********************** 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 64 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 TYR cc_start: 0.8197 (m-80) cc_final: 0.7071 (m-80) REVERT: C 246 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7476 (mpp) outliers start: 10 outliers final: 6 residues processed: 60 average time/residue: 0.4603 time to fit residues: 39.3030 Evaluate side-chains 52 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 314 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN C 314 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23748 Z= 0.188 Angle : 0.630 9.593 36292 Z= 0.319 Chirality : 0.032 0.246 4708 Planarity : 0.005 0.040 1430 Dihedral : 25.314 179.826 13552 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 3.66 % Allowed : 7.89 % Favored : 88.45 % 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: -2.93 (0.39), residues: 408 helix: -0.49 (0.33), residues: 219 sheet: -2.17 (0.85), residues: 36 loop : -4.14 (0.42), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 396 HIS 0.016 0.002 HIS C 314 PHE 0.021 0.002 PHE C 231 TYR 0.013 0.002 TYR C 143 ARG 0.005 0.001 ARG C 116 *********************** 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 61 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: C 65 PHE cc_start: 0.7946 (t80) cc_final: 0.7592 (t80) REVERT: C 116 ARG cc_start: 0.6854 (tpt-90) cc_final: 0.6593 (ttt90) REVERT: C 118 TYR cc_start: 0.7741 (m-80) cc_final: 0.7425 (m-80) REVERT: C 246 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7524 (mpp) REVERT: C 317 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6764 (tm-30) outliers start: 13 outliers final: 5 residues processed: 56 average time/residue: 0.4231 time to fit residues: 34.1332 Evaluate side-chains 53 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 349 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 59 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN C 63 HIS ** C 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23748 Z= 0.297 Angle : 0.704 9.298 36292 Z= 0.354 Chirality : 0.036 0.256 4708 Planarity : 0.005 0.034 1430 Dihedral : 25.356 178.398 13552 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 3.38 % Allowed : 9.30 % Favored : 87.32 % 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: -2.75 (0.39), residues: 408 helix: -0.34 (0.33), residues: 220 sheet: -2.22 (0.86), residues: 36 loop : -4.04 (0.42), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 204 HIS 0.007 0.002 HIS C 346 PHE 0.022 0.002 PHE C 231 TYR 0.021 0.003 TYR C 378 ARG 0.005 0.001 ARG C 157 *********************** 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 58 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.915 Fit side-chains REVERT: C 34 GLU cc_start: 0.7708 (tp30) cc_final: 0.7446 (tt0) REVERT: C 66 TYR cc_start: 0.7598 (m-80) cc_final: 0.6485 (m-80) REVERT: C 116 ARG cc_start: 0.7003 (tpt-90) cc_final: 0.6633 (ttt90) REVERT: C 203 GLU cc_start: 0.7502 (pm20) cc_final: 0.7269 (pt0) REVERT: C 246 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7507 (mpp) REVERT: C 397 HIS cc_start: 0.7895 (t-90) cc_final: 0.7606 (t-90) outliers start: 12 outliers final: 8 residues processed: 53 average time/residue: 0.4159 time to fit residues: 32.8565 Evaluate side-chains 52 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 167 CYS 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 282 GLU Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 429 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN ** C 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23748 Z= 0.287 Angle : 0.690 9.397 36292 Z= 0.347 Chirality : 0.035 0.252 4708 Planarity : 0.005 0.036 1430 Dihedral : 25.339 178.812 13552 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 3.66 % Allowed : 10.99 % Favored : 85.35 % 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: -2.59 (0.40), residues: 408 helix: -0.19 (0.34), residues: 220 sheet: -2.23 (0.86), residues: 36 loop : -3.97 (0.43), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 396 HIS 0.007 0.002 HIS C 346 PHE 0.024 0.002 PHE C 65 TYR 0.018 0.002 TYR C 378 ARG 0.005 0.001 ARG C 157 *********************** 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 54 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.873 Fit side-chains REVERT: C 66 TYR cc_start: 0.7653 (m-80) cc_final: 0.6392 (m-80) REVERT: C 203 GLU cc_start: 0.7546 (pm20) cc_final: 0.7294 (pt0) REVERT: C 246 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7521 (mpp) REVERT: C 300 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: C 317 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7125 (tm-30) REVERT: C 397 HIS cc_start: 0.7902 (t-90) cc_final: 0.7638 (t-90) outliers start: 13 outliers final: 8 residues processed: 50 average time/residue: 0.4404 time to fit residues: 32.0015 Evaluate side-chains 49 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 349 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 119 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN C 262 HIS ** C 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 23748 Z= 0.427 Angle : 0.832 9.352 36292 Z= 0.415 Chirality : 0.041 0.262 4708 Planarity : 0.006 0.061 1430 Dihedral : 25.561 178.268 13552 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.46 % Favored : 85.54 % Rotamer: Outliers : 4.51 % Allowed : 12.96 % Favored : 82.54 % 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: -2.97 (0.39), residues: 408 helix: -0.62 (0.33), residues: 220 sheet: -2.06 (0.86), residues: 36 loop : -4.03 (0.43), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 324 HIS 0.008 0.003 HIS C 346 PHE 0.040 0.003 PHE C 65 TYR 0.022 0.003 TYR C 378 ARG 0.016 0.001 ARG C 217 *********************** 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 58 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 42 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: C 66 TYR cc_start: 0.7603 (m-80) cc_final: 0.6727 (m-80) REVERT: C 246 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7473 (mpp) REVERT: C 300 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7965 (mp0) outliers start: 16 outliers final: 10 residues processed: 53 average time/residue: 0.3524 time to fit residues: 29.0424 Evaluate side-chains 52 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 429 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 67 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 119 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23748 Z= 0.167 Angle : 0.611 9.569 36292 Z= 0.308 Chirality : 0.031 0.242 4708 Planarity : 0.004 0.037 1430 Dihedral : 25.233 179.059 13552 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 2.82 % Allowed : 15.49 % Favored : 81.69 % 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: -2.44 (0.40), residues: 408 helix: -0.05 (0.34), residues: 219 sheet: -2.03 (0.86), residues: 36 loop : -3.94 (0.43), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 59 HIS 0.004 0.001 HIS C 314 PHE 0.026 0.002 PHE C 65 TYR 0.012 0.002 TYR C 109 ARG 0.006 0.000 ARG C 217 *********************** 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 54 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 58 GLN cc_start: 0.8677 (mt0) cc_final: 0.8475 (mt0) REVERT: C 246 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7585 (mpp) REVERT: C 317 GLU cc_start: 0.7337 (tm-30) cc_final: 0.7003 (tm-30) outliers start: 10 outliers final: 5 residues processed: 50 average time/residue: 0.3891 time to fit residues: 29.2273 Evaluate side-chains 48 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 421 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 262 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 23748 Z= 0.427 Angle : 0.802 9.213 36292 Z= 0.398 Chirality : 0.040 0.260 4708 Planarity : 0.006 0.055 1430 Dihedral : 25.433 178.745 13552 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.22 % Favored : 85.78 % Rotamer: Outliers : 3.38 % Allowed : 15.49 % 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: -2.91 (0.40), residues: 408 helix: -0.56 (0.34), residues: 219 sheet: -2.11 (0.86), residues: 36 loop : -3.99 (0.43), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 324 HIS 0.006 0.002 HIS C 346 PHE 0.022 0.003 PHE C 231 TYR 0.020 0.003 TYR C 378 ARG 0.006 0.001 ARG C 157 *********************** 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 56 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: C 66 TYR cc_start: 0.7760 (m-80) cc_final: 0.6684 (m-80) REVERT: C 246 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7519 (mpp) REVERT: C 300 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: C 397 HIS cc_start: 0.7952 (t-90) cc_final: 0.7702 (t-90) outliers start: 12 outliers final: 8 residues processed: 53 average time/residue: 0.4070 time to fit residues: 32.1172 Evaluate side-chains 52 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 456 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 100 optimal weight: 0.4980 chunk 105 optimal weight: 0.1980 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23748 Z= 0.138 Angle : 0.594 9.747 36292 Z= 0.298 Chirality : 0.029 0.236 4708 Planarity : 0.004 0.039 1430 Dihedral : 25.079 178.210 13552 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.97 % Allowed : 18.59 % Favored : 79.44 % 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: -2.16 (0.41), residues: 408 helix: 0.23 (0.35), residues: 218 sheet: -1.99 (0.87), residues: 36 loop : -3.86 (0.43), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 59 HIS 0.006 0.001 HIS C 202 PHE 0.014 0.002 PHE C 65 TYR 0.021 0.002 TYR C 66 ARG 0.005 0.001 ARG C 217 *********************** 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 53 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: C 66 TYR cc_start: 0.7403 (m-80) cc_final: 0.5900 (m-80) REVERT: C 246 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7716 (mtm) REVERT: C 317 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6898 (tm-30) REVERT: C 392 ASP cc_start: 0.7529 (m-30) cc_final: 0.7237 (t0) outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.3960 time to fit residues: 30.2158 Evaluate side-chains 51 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 421 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN C 262 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23748 Z= 0.285 Angle : 0.682 9.363 36292 Z= 0.341 Chirality : 0.034 0.255 4708 Planarity : 0.005 0.044 1430 Dihedral : 25.183 179.734 13552 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 2.54 % Allowed : 17.18 % Favored : 80.28 % 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: -2.39 (0.40), residues: 408 helix: -0.07 (0.35), residues: 219 sheet: -1.89 (0.87), residues: 36 loop : -3.87 (0.43), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 324 HIS 0.005 0.002 HIS C 346 PHE 0.019 0.002 PHE C 231 TYR 0.018 0.002 TYR C 66 ARG 0.004 0.001 ARG C 157 ********************** 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 54 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: C 66 TYR cc_start: 0.7577 (m-80) cc_final: 0.6693 (m-80) REVERT: C 246 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7568 (mpp) REVERT: C 300 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: C 317 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7086 (tm-30) REVERT: C 397 HIS cc_start: 0.7901 (t-90) cc_final: 0.7579 (t-90) outliers start: 9 outliers final: 5 residues processed: 51 average time/residue: 0.4318 time to fit residues: 32.2098 Evaluate side-chains 45 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 421 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN C 262 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.099797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.077090 restraints weight = 74144.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.078876 restraints weight = 29816.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.080095 restraints weight = 18393.599| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23748 Z= 0.182 Angle : 0.606 9.605 36292 Z= 0.305 Chirality : 0.030 0.245 4708 Planarity : 0.004 0.037 1430 Dihedral : 25.073 179.401 13552 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 1.97 % Allowed : 19.15 % Favored : 78.87 % 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: -2.05 (0.41), residues: 408 helix: 0.21 (0.35), residues: 219 sheet: -1.76 (0.88), residues: 36 loop : -3.72 (0.44), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 59 HIS 0.003 0.001 HIS C 314 PHE 0.016 0.001 PHE C 231 TYR 0.022 0.002 TYR C 66 ARG 0.004 0.000 ARG C 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2614.49 seconds wall clock time: 49 minutes 46.00 seconds (2986.00 seconds total)