Starting phenix.real_space_refine on Thu Jul 18 21:56:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn1_32619/07_2024/7wn1_32619.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn1_32619/07_2024/7wn1_32619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn1_32619/07_2024/7wn1_32619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn1_32619/07_2024/7wn1_32619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn1_32619/07_2024/7wn1_32619.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn1_32619/07_2024/7wn1_32619.cif" } resolution = 3.11 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= 0.033 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 2572 2.51 5 N 616 2.21 5 O 687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 89": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3901 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2953 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 1 Chain: "C" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'NOS%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 3.26, per 1000 atoms: 0.84 Number of scatterers: 3901 At special positions: 0 Unit cell: (110.39, 60.59, 64.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 687 8.00 N 616 7.00 C 2572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 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: 1.60 Conformation dependent library (CDL) restraints added in 704.9 milliseconds 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 914 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 64.3% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 31 through 59 removed outlier: 4.331A pdb=" N VAL A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TRP A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 83 removed outlier: 3.547A pdb=" N ASN A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 89 through 111 Processing helix chain 'A' and resid 112 through 144 Processing helix chain 'A' and resid 149 through 175 removed outlier: 3.802A pdb=" N GLN A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 210 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 239 through 257 removed outlier: 3.734A pdb=" N ILE A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.674A pdb=" N GLN A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 290 removed outlier: 3.759A pdb=" N THR A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.967A pdb=" N ASN A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 321 through 332 removed outlier: 3.538A pdb=" N TRP A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 369 removed outlier: 3.804A pdb=" N LEU A 350 " --> pdb=" O CYS A 346 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Proline residue: A 361 - end of helix removed outlier: 5.181A pdb=" N VAL A 366 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 400 removed outlier: 3.655A pdb=" N ILE A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'C' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY C 10 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ARG C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY C 10 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C 109 " --> pdb=" O THR C 99 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 823 1.33 - 1.45: 929 1.45 - 1.57: 2205 1.57 - 1.69: 2 1.69 - 1.81: 39 Bond restraints: 3998 Sorted by residual: bond pdb=" C1' NOS A 501 " pdb=" O4' NOS A 501 " ideal model delta sigma weight residual 1.415 1.600 -0.185 1.50e-02 4.44e+03 1.53e+02 bond pdb=" C1' NOS A 501 " pdb=" C2' NOS A 501 " ideal model delta sigma weight residual 1.526 1.346 0.180 1.50e-02 4.44e+03 1.44e+02 bond pdb=" C4' NOS A 501 " pdb=" O4' NOS A 501 " ideal model delta sigma weight residual 1.454 1.309 0.145 1.50e-02 4.44e+03 9.32e+01 bond pdb=" C2 NOS A 501 " pdb=" N3 NOS A 501 " ideal model delta sigma weight residual 1.293 1.444 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C4 NOS A 501 " pdb=" N3 NOS A 501 " ideal model delta sigma weight residual 1.347 1.497 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 3993 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.08: 87 107.08 - 113.80: 2264 113.80 - 120.52: 1589 120.52 - 127.25: 1448 127.25 - 133.97: 41 Bond angle restraints: 5429 Sorted by residual: angle pdb=" C3' NOS A 501 " pdb=" C2' NOS A 501 " pdb=" O2' NOS A 501 " ideal model delta sigma weight residual 114.60 107.68 6.92 1.50e+00 4.44e-01 2.13e+01 angle pdb=" C3' NOS A 501 " pdb=" C4' NOS A 501 " pdb=" C5' NOS A 501 " ideal model delta sigma weight residual 115.20 109.44 5.76 1.50e+00 4.44e-01 1.47e+01 angle pdb=" C1' NOS A 501 " pdb=" O4' NOS A 501 " pdb=" C4' NOS A 501 " ideal model delta sigma weight residual 109.70 106.15 3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" C2' NOS A 501 " pdb=" C1' NOS A 501 " pdb=" N9 NOS A 501 " ideal model delta sigma weight residual 114.00 108.75 5.25 1.50e+00 4.44e-01 1.23e+01 angle pdb=" C1' NOS A 501 " pdb=" C2' NOS A 501 " pdb=" C3' NOS A 501 " ideal model delta sigma weight residual 101.50 104.96 -3.46 1.00e+00 1.00e+00 1.20e+01 ... (remaining 5424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 2049 15.24 - 30.48: 201 30.48 - 45.71: 53 45.71 - 60.95: 17 60.95 - 76.19: 3 Dihedral angle restraints: 2323 sinusoidal: 899 harmonic: 1424 Sorted by residual: dihedral pdb=" C2' NOS A 501 " pdb=" C3' NOS A 501 " pdb=" C4' NOS A 501 " pdb=" O4' NOS A 501 " ideal model delta sinusoidal sigma weight residual 24.00 -2.88 26.88 1 8.00e+00 1.56e-02 1.62e+01 dihedral pdb=" C1' NOS A 501 " pdb=" C4' NOS A 501 " pdb=" O4' NOS A 501 " pdb=" C3' NOS A 501 " ideal model delta sinusoidal sigma weight residual 2.00 -22.80 24.80 1 8.00e+00 1.56e-02 1.38e+01 dihedral pdb=" CA LEU A 256 " pdb=" C LEU A 256 " pdb=" N PHE A 257 " pdb=" CA PHE A 257 " ideal model delta harmonic sigma weight residual -180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 2320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 372 0.031 - 0.061: 173 0.061 - 0.092: 57 0.092 - 0.122: 20 0.122 - 0.153: 8 Chirality restraints: 630 Sorted by residual: chirality pdb=" CB ILE A 193 " pdb=" CA ILE A 193 " pdb=" CG1 ILE A 193 " pdb=" CG2 ILE A 193 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA ASP A 147 " pdb=" N ASP A 147 " pdb=" C ASP A 147 " pdb=" CB ASP A 147 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA PHE A 307 " pdb=" N PHE A 307 " pdb=" C PHE A 307 " pdb=" CB PHE A 307 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 627 not shown) Planarity restraints: 665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 257 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 258 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 334 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO A 335 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 335 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 335 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 412 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.51e+00 pdb=" N PRO A 413 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 413 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 413 " -0.017 5.00e-02 4.00e+02 ... (remaining 662 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 835 2.78 - 3.31: 3841 3.31 - 3.84: 6568 3.84 - 4.37: 7875 4.37 - 4.90: 13686 Nonbonded interactions: 32805 Sorted by model distance: nonbonded pdb=" OH TYR A 65 " pdb=" OD1 ASP A 117 " model vdw 2.246 2.440 nonbonded pdb=" OG1 THR A 41 " pdb=" OD1 ASN A 209 " model vdw 2.256 2.440 nonbonded pdb=" O CYS A 395 " pdb=" OG1 THR A 399 " model vdw 2.283 2.440 nonbonded pdb=" O LEU A 256 " pdb=" N GLY A 261 " model vdw 2.320 2.520 nonbonded pdb=" NE2 GLN C 81 " pdb=" OD1 ASN C 83 " model vdw 2.320 2.520 ... (remaining 32800 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.570 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.007 0.185 3998 Z= 0.429 Angle : 0.648 10.003 5429 Z= 0.352 Chirality : 0.042 0.153 630 Planarity : 0.004 0.035 665 Dihedral : 13.827 76.187 1406 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.38), residues: 487 helix: 1.09 (0.30), residues: 285 sheet: 0.84 (0.64), residues: 58 loop : -0.10 (0.58), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 251 HIS 0.004 0.001 HIS A 334 PHE 0.016 0.001 PHE C 27 TYR 0.018 0.001 TYR C 102 ARG 0.002 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.463 Fit side-chains REVERT: A 175 VAL cc_start: 0.8097 (t) cc_final: 0.7828 (m) REVERT: A 303 LYS cc_start: 0.8628 (tppt) cc_final: 0.8418 (tppt) REVERT: A 407 ASN cc_start: 0.8197 (t0) cc_final: 0.7963 (t0) REVERT: C 94 TYR cc_start: 0.8213 (m-10) cc_final: 0.8003 (m-10) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1548 time to fit residues: 14.3141 Evaluate side-chains 62 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 23 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3998 Z= 0.206 Angle : 0.566 6.440 5429 Z= 0.306 Chirality : 0.042 0.142 630 Planarity : 0.004 0.033 665 Dihedral : 5.615 37.796 540 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.09 % Allowed : 6.05 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.38), residues: 487 helix: 1.58 (0.29), residues: 288 sheet: 1.00 (0.64), residues: 58 loop : -0.20 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 251 HIS 0.003 0.001 HIS A 180 PHE 0.017 0.001 PHE C 27 TYR 0.019 0.001 TYR C 102 ARG 0.002 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.452 Fit side-chains REVERT: A 303 LYS cc_start: 0.8642 (tppt) cc_final: 0.8440 (tppt) REVERT: A 407 ASN cc_start: 0.8195 (t0) cc_final: 0.7977 (t0) outliers start: 9 outliers final: 4 residues processed: 65 average time/residue: 0.1654 time to fit residues: 13.5083 Evaluate side-chains 61 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 82 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 54 ASN A 209 ASN A 284 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 3998 Z= 0.442 Angle : 0.669 6.136 5429 Z= 0.364 Chirality : 0.048 0.148 630 Planarity : 0.004 0.036 665 Dihedral : 5.684 35.241 540 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.02 % Allowed : 10.47 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.37), residues: 487 helix: 1.29 (0.29), residues: 286 sheet: 0.78 (0.63), residues: 59 loop : -0.56 (0.53), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 251 HIS 0.006 0.001 HIS A 180 PHE 0.019 0.002 PHE C 27 TYR 0.024 0.002 TYR C 102 ARG 0.005 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.415 Fit side-chains REVERT: A 303 LYS cc_start: 0.8682 (tppt) cc_final: 0.8466 (tppt) REVERT: A 407 ASN cc_start: 0.8249 (t0) cc_final: 0.8043 (t0) REVERT: C 19 ARG cc_start: 0.8584 (mtp85) cc_final: 0.8244 (mtp-110) outliers start: 13 outliers final: 9 residues processed: 64 average time/residue: 0.1658 time to fit residues: 13.3428 Evaluate side-chains 67 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.0870 chunk 42 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 54 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3998 Z= 0.174 Angle : 0.526 6.781 5429 Z= 0.284 Chirality : 0.043 0.261 630 Planarity : 0.004 0.033 665 Dihedral : 5.155 29.904 540 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.02 % Allowed : 10.70 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.38), residues: 487 helix: 1.71 (0.29), residues: 289 sheet: 0.96 (0.65), residues: 58 loop : -0.09 (0.57), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.015 0.001 PHE C 27 TYR 0.016 0.001 TYR C 102 ARG 0.002 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.473 Fit side-chains REVERT: A 303 LYS cc_start: 0.8665 (tppt) cc_final: 0.8459 (tppt) REVERT: C 19 ARG cc_start: 0.8557 (mtp85) cc_final: 0.8163 (mtp-110) outliers start: 13 outliers final: 8 residues processed: 67 average time/residue: 0.1586 time to fit residues: 13.6411 Evaluate side-chains 67 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3998 Z= 0.178 Angle : 0.523 6.414 5429 Z= 0.279 Chirality : 0.042 0.225 630 Planarity : 0.004 0.033 665 Dihedral : 4.968 27.809 540 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.09 % Allowed : 13.95 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.38), residues: 487 helix: 1.89 (0.29), residues: 289 sheet: 0.98 (0.65), residues: 58 loop : -0.04 (0.57), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.015 0.001 PHE C 27 TYR 0.018 0.001 TYR C 102 ARG 0.001 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.397 Fit side-chains REVERT: A 303 LYS cc_start: 0.8672 (tppt) cc_final: 0.8461 (tppt) REVERT: C 19 ARG cc_start: 0.8539 (mtp85) cc_final: 0.8137 (mtp-110) outliers start: 9 outliers final: 9 residues processed: 62 average time/residue: 0.1675 time to fit residues: 13.2264 Evaluate side-chains 66 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.0870 chunk 39 optimal weight: 7.9990 chunk 21 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3998 Z= 0.179 Angle : 0.519 7.224 5429 Z= 0.277 Chirality : 0.042 0.197 630 Planarity : 0.004 0.033 665 Dihedral : 4.855 25.995 540 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.95 % Allowed : 12.56 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.38), residues: 487 helix: 1.84 (0.29), residues: 293 sheet: 0.98 (0.65), residues: 58 loop : -0.08 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.013 0.001 PHE C 27 TYR 0.019 0.001 TYR C 102 ARG 0.001 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 56 time to evaluate : 0.460 Fit side-chains REVERT: A 303 LYS cc_start: 0.8672 (tppt) cc_final: 0.8448 (tppt) REVERT: A 368 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.6245 (mp0) REVERT: C 19 ARG cc_start: 0.8536 (mtp85) cc_final: 0.8126 (mtp-110) outliers start: 17 outliers final: 10 residues processed: 64 average time/residue: 0.1548 time to fit residues: 12.6236 Evaluate side-chains 68 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 47 optimal weight: 0.2980 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3998 Z= 0.185 Angle : 0.518 6.600 5429 Z= 0.276 Chirality : 0.042 0.183 630 Planarity : 0.004 0.033 665 Dihedral : 4.790 26.552 540 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.49 % Allowed : 13.02 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.38), residues: 487 helix: 2.00 (0.29), residues: 289 sheet: 1.03 (0.65), residues: 58 loop : -0.00 (0.58), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.013 0.001 PHE C 27 TYR 0.019 0.001 TYR C 102 ARG 0.001 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.439 Fit side-chains REVERT: A 368 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.6246 (mp0) REVERT: C 19 ARG cc_start: 0.8533 (mtp85) cc_final: 0.8119 (mtp-110) outliers start: 15 outliers final: 11 residues processed: 66 average time/residue: 0.1534 time to fit residues: 12.8259 Evaluate side-chains 68 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 0.0270 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3998 Z= 0.161 Angle : 0.508 6.528 5429 Z= 0.270 Chirality : 0.041 0.174 630 Planarity : 0.004 0.033 665 Dihedral : 4.666 27.422 540 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.26 % Allowed : 14.42 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.39), residues: 487 helix: 2.01 (0.29), residues: 292 sheet: 1.14 (0.66), residues: 58 loop : -0.13 (0.59), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 251 HIS 0.002 0.001 HIS A 334 PHE 0.012 0.001 PHE C 27 TYR 0.017 0.001 TYR C 102 ARG 0.001 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.461 Fit side-chains REVERT: A 187 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8296 (mtpt) REVERT: A 368 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.6245 (mp0) outliers start: 14 outliers final: 10 residues processed: 65 average time/residue: 0.1538 time to fit residues: 12.6846 Evaluate side-chains 68 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.0470 chunk 43 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3998 Z= 0.177 Angle : 0.509 6.395 5429 Z= 0.272 Chirality : 0.041 0.176 630 Planarity : 0.004 0.033 665 Dihedral : 4.628 28.035 540 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.26 % Allowed : 14.65 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.38), residues: 487 helix: 1.99 (0.29), residues: 293 sheet: 1.22 (0.66), residues: 58 loop : -0.08 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.013 0.001 PHE C 27 TYR 0.018 0.001 TYR C 102 ARG 0.001 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.449 Fit side-chains REVERT: A 187 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8308 (mtpt) REVERT: A 368 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.6128 (mp0) outliers start: 14 outliers final: 10 residues processed: 65 average time/residue: 0.1596 time to fit residues: 13.1712 Evaluate side-chains 71 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3998 Z= 0.209 Angle : 0.525 6.281 5429 Z= 0.281 Chirality : 0.042 0.173 630 Planarity : 0.004 0.034 665 Dihedral : 4.700 27.036 540 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.26 % Allowed : 14.65 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.38), residues: 487 helix: 1.91 (0.29), residues: 293 sheet: 1.22 (0.66), residues: 58 loop : -0.13 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.013 0.001 PHE C 27 TYR 0.020 0.001 TYR C 102 ARG 0.001 0.000 ARG A 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.449 Fit side-chains REVERT: A 368 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.6026 (mp0) outliers start: 14 outliers final: 11 residues processed: 63 average time/residue: 0.1620 time to fit residues: 12.9532 Evaluate side-chains 67 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.0570 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.102066 restraints weight = 5107.824| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.57 r_work: 0.3106 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3998 Z= 0.190 Angle : 0.521 7.305 5429 Z= 0.278 Chirality : 0.042 0.170 630 Planarity : 0.004 0.035 665 Dihedral : 4.660 26.573 540 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.02 % Allowed : 14.65 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.38), residues: 487 helix: 1.97 (0.29), residues: 293 sheet: 1.21 (0.66), residues: 58 loop : -0.15 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.012 0.001 PHE C 27 TYR 0.019 0.001 TYR C 102 ARG 0.001 0.000 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1260.95 seconds wall clock time: 23 minutes 8.09 seconds (1388.09 seconds total)