Starting phenix.real_space_refine on Thu Apr 11 03:47:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6me0_9105/04_2024/6me0_9105.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6me0_9105/04_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_9105/04_2024/6me0_9105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6me0_9105/04_2024/6me0_9105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6me0_9105/04_2024/6me0_9105.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6me0_9105/04_2024/6me0_9105.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 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 Residue "C ARG 413": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 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: 12.59, per 1000 atoms: 0.58 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 - 3.50 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: 14.10 Conformation dependent library (CDL) restraints added in 819.8 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: 11.22 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: 15.84 Time building geometry restraints manager: 14.81 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: 97.07 - 105.18: 4081 105.18 - 113.29: 14716 113.29 - 121.40: 11535 121.40 - 129.51: 5327 129.51 - 137.62: 633 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 2.520 nonbonded pdb=" O2 U A 1 " pdb=" N1 G A 865 " model vdw 1.696 2.520 ... (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 ========== 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: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 13.810 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 77.550 Find NCS groups from input model: 0.400 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: 99.110 ------------------------------------------------------------------------------- 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 : 1.050 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: 0.5829 time to fit residues: 73.9618 Evaluate side-chains 52 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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: 2.9990 chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 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: 0.9980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN ** C 174 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1499 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= 0.269 Angle : 0.700 8.954 36292 Z= 0.355 Chirality : 0.036 0.256 4708 Planarity : 0.005 0.040 1430 Dihedral : 25.506 178.579 13552 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 2.54 % Allowed : 6.48 % Favored : 90.99 % 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: -3.69 (0.36), residues: 408 helix: -1.20 (0.31), residues: 216 sheet: -2.13 (0.77), residues: 36 loop : -4.38 (0.39), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C 396 HIS 0.009 0.002 HIS C 346 PHE 0.033 0.003 PHE C 231 TYR 0.018 0.003 TYR C 66 ARG 0.008 0.001 ARG C 116 *********************** 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 65 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 51 TRP cc_start: 0.8915 (m100) cc_final: 0.8404 (m-10) REVERT: C 110 LYS cc_start: 0.8750 (mmmt) cc_final: 0.8519 (tppt) REVERT: C 118 TYR cc_start: 0.8111 (m-80) cc_final: 0.7211 (m-80) REVERT: C 163 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.8094 (ttm-80) REVERT: C 203 GLU cc_start: 0.7837 (mp0) cc_final: 0.7569 (mp0) REVERT: C 246 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7439 (mpp) REVERT: C 317 GLU cc_start: 0.7448 (tm-30) cc_final: 0.6997 (tm-30) outliers start: 9 outliers final: 4 residues processed: 62 average time/residue: 0.4721 time to fit residues: 41.6175 Evaluate side-chains 49 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 284 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 121 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23748 Z= 0.227 Angle : 0.643 9.514 36292 Z= 0.325 Chirality : 0.033 0.246 4708 Planarity : 0.005 0.034 1430 Dihedral : 25.350 179.868 13552 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 4.23 % Allowed : 8.73 % 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: -2.89 (0.39), residues: 408 helix: -0.40 (0.34), residues: 217 sheet: -1.95 (0.86), residues: 36 loop : -4.24 (0.41), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 396 HIS 0.003 0.001 HIS C 346 PHE 0.023 0.003 PHE C 231 TYR 0.018 0.003 TYR C 66 ARG 0.004 0.001 ARG C 115 *********************** 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 63 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: C 110 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8488 (tppt) REVERT: C 163 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.8021 (ttm-80) REVERT: C 246 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7494 (mpp) REVERT: C 317 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7126 (tm-30) outliers start: 15 outliers final: 7 residues processed: 58 average time/residue: 0.4469 time to fit residues: 37.7151 Evaluate side-chains 50 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 271 ILE Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 314 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23748 Z= 0.230 Angle : 0.636 9.487 36292 Z= 0.320 Chirality : 0.033 0.237 4708 Planarity : 0.004 0.038 1430 Dihedral : 25.281 179.997 13552 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 3.10 % Allowed : 11.83 % Favored : 85.07 % 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: -2.58 (0.40), residues: 408 helix: -0.11 (0.34), residues: 217 sheet: -2.01 (0.88), residues: 36 loop : -4.11 (0.41), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 396 HIS 0.005 0.002 HIS C 346 PHE 0.021 0.002 PHE C 231 TYR 0.016 0.002 TYR C 378 ARG 0.004 0.000 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 53 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: C 110 LYS cc_start: 0.8723 (mmmt) cc_final: 0.8492 (tppt) REVERT: C 203 GLU cc_start: 0.7620 (pm20) cc_final: 0.7275 (pt0) REVERT: C 246 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7529 (mpp) REVERT: C 317 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7170 (tm-30) outliers start: 11 outliers final: 7 residues processed: 48 average time/residue: 0.4540 time to fit residues: 31.5531 Evaluate side-chains 45 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 89 optimal weight: 0.0470 chunk 49 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 23748 Z= 0.269 Angle : 0.664 9.543 36292 Z= 0.333 Chirality : 0.034 0.240 4708 Planarity : 0.005 0.052 1430 Dihedral : 25.277 179.728 13552 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 3.66 % Allowed : 11.83 % Favored : 84.51 % 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: -2.57 (0.40), residues: 408 helix: -0.14 (0.34), residues: 217 sheet: -1.90 (0.89), residues: 36 loop : -4.05 (0.42), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 396 HIS 0.006 0.002 HIS C 346 PHE 0.021 0.002 PHE C 231 TYR 0.020 0.002 TYR C 378 ARG 0.008 0.001 ARG C 163 *********************** 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 53 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: C 246 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7555 (mpp) REVERT: C 317 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7423 (tm-30) outliers start: 13 outliers final: 7 residues processed: 48 average time/residue: 0.4071 time to fit residues: 29.0152 Evaluate side-chains 45 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 284 LYS Chi-restraints excluded: chain C residue 314 HIS 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: 6.9990 chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 23748 Z= 0.392 Angle : 0.775 9.251 36292 Z= 0.386 Chirality : 0.039 0.258 4708 Planarity : 0.005 0.035 1430 Dihedral : 25.484 179.165 13552 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.46 % Favored : 85.54 % Rotamer: Outliers : 4.23 % Allowed : 12.96 % Favored : 82.82 % 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: -2.78 (0.39), residues: 408 helix: -0.34 (0.34), residues: 215 sheet: -1.73 (0.89), residues: 36 loop : -4.13 (0.41), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 204 HIS 0.005 0.002 HIS C 63 PHE 0.043 0.003 PHE C 65 TYR 0.019 0.003 TYR C 378 ARG 0.006 0.001 ARG C 163 *********************** 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 56 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 246 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7454 (mpp) REVERT: C 397 HIS cc_start: 0.7811 (t-90) cc_final: 0.7574 (t-90) outliers start: 15 outliers final: 8 residues processed: 50 average time/residue: 0.4430 time to fit residues: 32.2802 Evaluate side-chains 48 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 314 HIS 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: 0.9980 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 67 optimal weight: 20.0000 chunk 100 optimal weight: 0.3980 chunk 66 optimal weight: 20.0000 chunk 119 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23748 Z= 0.181 Angle : 0.604 9.649 36292 Z= 0.303 Chirality : 0.031 0.225 4708 Planarity : 0.005 0.072 1430 Dihedral : 25.170 179.203 13552 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 3.10 % Allowed : 15.21 % 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: -2.32 (0.41), residues: 408 helix: 0.03 (0.35), residues: 218 sheet: -1.63 (0.92), residues: 36 loop : -3.96 (0.42), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 59 HIS 0.004 0.001 HIS C 379 PHE 0.024 0.002 PHE C 65 TYR 0.016 0.002 TYR C 329 ARG 0.005 0.000 ARG C 163 *********************** 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 47 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 36 time to evaluate : 1.031 Fit side-chains REVERT: C 66 TYR cc_start: 0.7444 (m-80) cc_final: 0.5684 (m-80) REVERT: C 246 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7523 (mpp) REVERT: C 300 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7392 (mp0) outliers start: 11 outliers final: 7 residues processed: 43 average time/residue: 0.4559 time to fit residues: 29.2371 Evaluate side-chains 44 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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 314 HIS Chi-restraints excluded: chain C residue 349 ILE 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: 10.9990 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: 0.2980 chunk 108 optimal weight: 2.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 23748 Z= 0.413 Angle : 0.785 9.278 36292 Z= 0.390 Chirality : 0.039 0.254 4708 Planarity : 0.005 0.034 1430 Dihedral : 25.405 179.332 13552 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % Rotamer: Outliers : 4.51 % Allowed : 15.77 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.40), residues: 408 helix: -0.47 (0.34), residues: 218 sheet: -1.54 (0.95), residues: 36 loop : -4.03 (0.42), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 204 HIS 0.007 0.002 HIS C 346 PHE 0.021 0.003 PHE C 231 TYR 0.021 0.003 TYR C 143 ARG 0.008 0.001 ARG C 163 *********************** 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: 16 poor density : 40 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 246 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7504 (mpp) REVERT: C 300 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: C 397 HIS cc_start: 0.7802 (t-90) cc_final: 0.7544 (t-90) outliers start: 16 outliers final: 11 residues processed: 51 average time/residue: 0.4500 time to fit residues: 33.7039 Evaluate side-chains 51 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 38 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 184 CYS Chi-restraints excluded: chain C residue 189 LEU 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 300 GLU Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 349 ILE 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: 0.6980 chunk 111 optimal weight: 0.5980 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: 0.6980 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23748 Z= 0.133 Angle : 0.579 9.607 36292 Z= 0.292 Chirality : 0.030 0.225 4708 Planarity : 0.004 0.035 1430 Dihedral : 25.030 177.682 13552 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.54 % Allowed : 17.46 % Favored : 80.00 % 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: 0.23 (0.35), residues: 219 sheet: -1.53 (0.92), residues: 36 loop : -3.82 (0.42), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 59 HIS 0.004 0.001 HIS C 379 PHE 0.013 0.002 PHE C 231 TYR 0.021 0.002 TYR C 66 ARG 0.008 0.001 ARG C 105 *********************** 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 56 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: C 66 TYR cc_start: 0.7429 (m-80) cc_final: 0.5867 (m-80) REVERT: C 246 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7713 (mtm) REVERT: C 296 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6161 (mt-10) REVERT: C 300 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7352 (mp0) outliers start: 9 outliers final: 5 residues processed: 52 average time/residue: 0.4243 time to fit residues: 32.8410 Evaluate side-chains 51 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 184 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 117 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 HIS ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 23748 Z= 0.279 Angle : 0.655 9.560 36292 Z= 0.327 Chirality : 0.034 0.229 4708 Planarity : 0.005 0.034 1430 Dihedral : 25.116 179.573 13552 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 3.10 % Allowed : 17.75 % Favored : 79.15 % 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: -2.13 (0.41), residues: 408 helix: 0.14 (0.35), residues: 219 sheet: -1.43 (0.94), residues: 36 loop : -3.86 (0.43), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 51 HIS 0.005 0.002 HIS C 346 PHE 0.019 0.002 PHE C 231 TYR 0.017 0.002 TYR C 378 ARG 0.008 0.001 ARG C 105 ********************** 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 48 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: C 246 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7529 (mpp) REVERT: C 300 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7478 (mp0) outliers start: 11 outliers final: 8 residues processed: 45 average time/residue: 0.3989 time to fit residues: 27.6689 Evaluate side-chains 46 residues out of total 355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 184 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 314 HIS Chi-restraints excluded: chain C residue 349 ILE 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: 2.9990 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 HIS ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.098453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.075774 restraints weight = 74033.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.077535 restraints weight = 30295.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.078547 restraints weight = 18907.518| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23748 Z= 0.244 Angle : 0.637 9.523 36292 Z= 0.319 Chirality : 0.032 0.228 4708 Planarity : 0.004 0.036 1430 Dihedral : 25.128 179.587 13552 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 3.66 % Allowed : 17.75 % Favored : 78.59 % 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: -2.07 (0.41), residues: 408 helix: 0.19 (0.35), residues: 219 sheet: -1.41 (0.93), residues: 36 loop : -3.82 (0.43), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 396 HIS 0.004 0.002 HIS C 63 PHE 0.018 0.002 PHE C 231 TYR 0.019 0.003 TYR C 143 ARG 0.008 0.001 ARG C 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2677.66 seconds wall clock time: 52 minutes 20.65 seconds (3140.65 seconds total)