Starting phenix.real_space_refine on Thu Jul 18 19:42:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znd_60268/07_2024/8znd_60268.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znd_60268/07_2024/8znd_60268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znd_60268/07_2024/8znd_60268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znd_60268/07_2024/8znd_60268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znd_60268/07_2024/8znd_60268.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8znd_60268/07_2024/8znd_60268.cif" } resolution = 2.53 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= 0.002 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2104 2.51 5 N 563 2.21 5 O 650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 5": "OD1" <-> "OD2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A ARG 396": "NH1" <-> "NH2" 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: 3334 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3262 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 395} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 72 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1, 'water': 24} Link IDs: {None: 24} Time building chain proxies: 2.72, per 1000 atoms: 0.82 Number of scatterers: 3334 At special positions: 0 Unit cell: (66.176, 63.92, 70.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 650 8.00 N 563 7.00 C 2104 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: 1.41 Conformation dependent library (CDL) restraints added in 575.4 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 3 sheets defined 56.2% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.681A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.551A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.728A pdb=" N TYR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.556A pdb=" N LEU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 323 through 334 removed outlier: 4.023A pdb=" N ASP A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 365 through 392 Processing helix chain 'A' and resid 394 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.643A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 45 removed outlier: 4.643A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 279 removed outlier: 3.558A pdb=" N VAL A 242 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS A 214 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA A 293 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA A 216 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 194 hydrogen bonds defined for protein. 555 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: 0.90 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1069 1.34 - 1.46: 465 1.46 - 1.57: 1820 1.57 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3386 Sorted by residual: bond pdb=" O2B NDP A 500 " pdb=" P2B NDP A 500 " ideal model delta sigma weight residual 1.833 1.607 0.226 3.80e-02 6.93e+02 3.53e+01 bond pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 1.757 1.596 0.161 3.50e-02 8.16e+02 2.13e+01 bond pdb=" N TYR A 250 " pdb=" CA TYR A 250 " ideal model delta sigma weight residual 1.455 1.413 0.042 1.25e-02 6.40e+03 1.15e+01 bond pdb=" C2B NDP A 500 " pdb=" O2B NDP A 500 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.90e-02 1.19e+03 9.52e+00 bond pdb=" CA TYR A 250 " pdb=" C TYR A 250 " ideal model delta sigma weight residual 1.520 1.487 0.034 1.22e-02 6.72e+03 7.60e+00 ... (remaining 3381 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.78: 123 106.78 - 113.61: 1848 113.61 - 120.44: 1293 120.44 - 127.28: 1288 127.28 - 134.11: 46 Bond angle restraints: 4598 Sorted by residual: angle pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 107.74 129.93 -22.19 1.95e+00 2.62e-01 1.29e+02 angle pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " ideal model delta sigma weight residual 103.84 119.43 -15.59 1.91e+00 2.73e-01 6.63e+01 angle pdb=" C5D NDP A 500 " pdb=" O5D NDP A 500 " pdb=" PN NDP A 500 " ideal model delta sigma weight residual 104.93 118.60 -13.67 2.66e+00 1.41e-01 2.64e+01 angle pdb=" O2N NDP A 500 " pdb=" PN NDP A 500 " pdb=" O5D NDP A 500 " ideal model delta sigma weight residual 100.52 109.34 -8.82 1.91e+00 2.74e-01 2.13e+01 angle pdb=" O1X NDP A 500 " pdb=" P2B NDP A 500 " pdb=" O3X NDP A 500 " ideal model delta sigma weight residual 117.46 112.28 5.18 1.17e+00 7.36e-01 1.97e+01 ... (remaining 4593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 1872 23.43 - 46.87: 110 46.87 - 70.30: 17 70.30 - 93.73: 9 93.73 - 117.16: 1 Dihedral angle restraints: 2009 sinusoidal: 820 harmonic: 1189 Sorted by residual: dihedral pdb=" C5B NDP A 500 " pdb=" O5B NDP A 500 " pdb=" PA NDP A 500 " pdb=" O3 NDP A 500 " ideal model delta sinusoidal sigma weight residual 175.04 57.88 117.16 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" CA PHE A 341 " pdb=" C PHE A 341 " pdb=" N LEU A 342 " pdb=" CA LEU A 342 " ideal model delta harmonic sigma weight residual 180.00 162.32 17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CB GLU A 288 " pdb=" CG GLU A 288 " pdb=" CD GLU A 288 " pdb=" OE1 GLU A 288 " ideal model delta sinusoidal sigma weight residual 0.00 -89.63 89.63 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 2006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 381 0.047 - 0.093: 79 0.093 - 0.140: 36 0.140 - 0.186: 2 0.186 - 0.233: 3 Chirality restraints: 501 Sorted by residual: chirality pdb=" C4D NDP A 500 " pdb=" C3D NDP A 500 " pdb=" C5D NDP A 500 " pdb=" O4D NDP A 500 " both_signs ideal model delta sigma weight residual False -2.71 -2.48 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TYR A 250 " pdb=" N TYR A 250 " pdb=" C TYR A 250 " pdb=" CB TYR A 250 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1B NDP A 500 " pdb=" C2B NDP A 500 " pdb=" N9A NDP A 500 " pdb=" O4B NDP A 500 " both_signs ideal model delta sigma weight residual False 2.59 2.40 0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 498 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 500 " 0.018 2.00e-02 2.50e+03 3.11e-02 9.68e+00 pdb=" C5N NDP A 500 " -0.039 2.00e-02 2.50e+03 pdb=" C6N NDP A 500 " 0.040 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP A 500 " 0.031 2.00e-02 2.50e+03 1.92e-02 4.62e+00 pdb=" C3N NDP A 500 " 0.004 2.00e-02 2.50e+03 pdb=" C4N NDP A 500 " 0.005 2.00e-02 2.50e+03 pdb=" C7N NDP A 500 " -0.016 2.00e-02 2.50e+03 pdb=" N1N NDP A 500 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO A 142 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.025 5.00e-02 4.00e+02 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1217 2.89 - 3.39: 3334 3.39 - 3.90: 6075 3.90 - 4.40: 6964 4.40 - 4.90: 11339 Nonbonded interactions: 28929 Sorted by model distance: nonbonded pdb=" NE ARG A 73 " pdb=" OE1 GLU A 78 " model vdw 2.392 2.520 nonbonded pdb=" O VAL A 401 " pdb=" OG SER A 405 " model vdw 2.402 2.440 nonbonded pdb=" OD1 ASP A 5 " pdb=" OG SER A 81 " model vdw 2.440 2.440 nonbonded pdb=" N ASP A 145 " pdb=" OG1 THR A 148 " model vdw 2.495 2.520 nonbonded pdb=" NZ LYS A 177 " pdb=" OD1 ASN A 358 " model vdw 2.504 2.520 ... (remaining 28924 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: 0.700 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.340 Find NCS groups from input model: 0.030 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:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 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 0.226 3386 Z= 0.501 Angle : 0.927 22.188 4598 Z= 0.525 Chirality : 0.048 0.233 501 Planarity : 0.005 0.047 586 Dihedral : 15.596 117.160 1251 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.88 % Allowed : 0.59 % Favored : 98.53 % 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: 0.95 (0.42), residues: 414 helix: 2.03 (0.35), residues: 202 sheet: -0.23 (0.63), residues: 72 loop : -0.97 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.002 0.001 HIS A 61 PHE 0.015 0.002 PHE A 341 TYR 0.015 0.002 TYR A 363 ARG 0.004 0.000 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.392 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 84 average time/residue: 1.5116 time to fit residues: 129.8290 Evaluate side-chains 59 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3386 Z= 0.138 Angle : 0.445 4.372 4598 Z= 0.237 Chirality : 0.041 0.130 501 Planarity : 0.005 0.044 586 Dihedral : 6.631 100.711 462 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.18 % Allowed : 11.50 % Favored : 87.32 % 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: 1.15 (0.42), residues: 414 helix: 2.13 (0.35), residues: 208 sheet: -0.10 (0.65), residues: 73 loop : -0.92 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.013 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.007 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.387 Fit side-chains REVERT: A 271 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8340 (ttmt) outliers start: 4 outliers final: 1 residues processed: 69 average time/residue: 1.3015 time to fit residues: 92.2663 Evaluate side-chains 62 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 271 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3386 Z= 0.223 Angle : 0.478 4.519 4598 Z= 0.255 Chirality : 0.043 0.129 501 Planarity : 0.005 0.045 586 Dihedral : 6.487 89.900 462 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.18 % Allowed : 12.39 % Favored : 86.43 % 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: 1.17 (0.43), residues: 414 helix: 2.06 (0.35), residues: 209 sheet: 0.23 (0.65), residues: 70 loop : -0.99 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 PHE 0.013 0.001 PHE A 341 TYR 0.014 0.001 TYR A 363 ARG 0.007 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.392 Fit side-chains REVERT: A 246 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7153 (mpt180) outliers start: 4 outliers final: 1 residues processed: 61 average time/residue: 1.5246 time to fit residues: 95.2279 Evaluate side-chains 55 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 246 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 0.0770 chunk 19 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3386 Z= 0.121 Angle : 0.412 4.360 4598 Z= 0.218 Chirality : 0.040 0.126 501 Planarity : 0.004 0.046 586 Dihedral : 6.029 83.269 462 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.47 % Allowed : 12.98 % Favored : 85.55 % 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: 1.37 (0.43), residues: 414 helix: 2.22 (0.35), residues: 209 sheet: 0.16 (0.65), residues: 73 loop : -0.80 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.002 0.000 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.009 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.365 Fit side-chains REVERT: A 246 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7346 (mpt180) outliers start: 5 outliers final: 2 residues processed: 64 average time/residue: 1.4869 time to fit residues: 97.4584 Evaluate side-chains 62 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 277 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3386 Z= 0.206 Angle : 0.459 4.536 4598 Z= 0.244 Chirality : 0.042 0.126 501 Planarity : 0.005 0.046 586 Dihedral : 6.034 80.291 462 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.77 % Allowed : 14.16 % Favored : 84.07 % 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: 1.37 (0.43), residues: 414 helix: 2.19 (0.35), residues: 209 sheet: 0.17 (0.65), residues: 73 loop : -0.75 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.002 0.001 HIS A 388 PHE 0.012 0.001 PHE A 341 TYR 0.013 0.001 TYR A 363 ARG 0.008 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.351 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 62 average time/residue: 1.4396 time to fit residues: 91.4667 Evaluate side-chains 66 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 277 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3386 Z= 0.163 Angle : 0.438 4.466 4598 Z= 0.232 Chirality : 0.041 0.127 501 Planarity : 0.005 0.047 586 Dihedral : 5.812 75.696 462 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.47 % Allowed : 14.75 % Favored : 83.78 % 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: 1.41 (0.43), residues: 414 helix: 2.22 (0.35), residues: 210 sheet: 0.20 (0.65), residues: 73 loop : -0.76 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.002 0.000 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.011 0.001 TYR A 363 ARG 0.009 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.407 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 65 average time/residue: 1.4571 time to fit residues: 96.9644 Evaluate side-chains 64 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3386 Z= 0.196 Angle : 0.457 4.525 4598 Z= 0.243 Chirality : 0.042 0.127 501 Planarity : 0.005 0.047 586 Dihedral : 5.746 72.420 462 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.77 % Allowed : 15.34 % Favored : 82.89 % 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: 1.38 (0.43), residues: 414 helix: 2.19 (0.35), residues: 210 sheet: 0.17 (0.65), residues: 73 loop : -0.74 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.012 0.001 PHE A 341 TYR 0.013 0.001 TYR A 363 ARG 0.009 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.290 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 67 average time/residue: 1.5540 time to fit residues: 106.5566 Evaluate side-chains 63 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 269 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3386 Z= 0.146 Angle : 0.430 4.447 4598 Z= 0.227 Chirality : 0.041 0.127 501 Planarity : 0.004 0.047 586 Dihedral : 5.466 67.447 462 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.47 % Allowed : 15.04 % Favored : 83.48 % 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: 1.50 (0.43), residues: 414 helix: 2.28 (0.35), residues: 210 sheet: 0.23 (0.65), residues: 73 loop : -0.69 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.001 0.000 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.009 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.392 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 66 average time/residue: 1.4052 time to fit residues: 95.0588 Evaluate side-chains 65 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 269 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3386 Z= 0.205 Angle : 0.470 4.538 4598 Z= 0.250 Chirality : 0.042 0.127 501 Planarity : 0.005 0.048 586 Dihedral : 5.501 65.283 462 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.88 % Allowed : 15.93 % Favored : 83.19 % 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: 1.48 (0.43), residues: 414 helix: 2.24 (0.35), residues: 209 sheet: 0.31 (0.66), residues: 72 loop : -0.67 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 382 HIS 0.007 0.001 HIS A 267 PHE 0.012 0.001 PHE A 341 TYR 0.013 0.001 TYR A 363 ARG 0.009 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.393 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 65 average time/residue: 1.5136 time to fit residues: 100.7713 Evaluate side-chains 63 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 269 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 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 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3386 Z= 0.128 Angle : 0.425 4.574 4598 Z= 0.223 Chirality : 0.040 0.127 501 Planarity : 0.004 0.046 586 Dihedral : 4.947 54.514 462 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.59 % Allowed : 17.40 % Favored : 82.01 % 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: 1.62 (0.43), residues: 414 helix: 2.37 (0.35), residues: 210 sheet: 0.29 (0.66), residues: 73 loop : -0.58 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 92 HIS 0.008 0.001 HIS A 267 PHE 0.010 0.001 PHE A 341 TYR 0.008 0.001 TYR A 363 ARG 0.009 0.000 ARG A 370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.405 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 67 average time/residue: 1.3773 time to fit residues: 94.7002 Evaluate side-chains 65 residues out of total 339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 269 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 9.9990 chunk 1 optimal weight: 0.0020 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.088962 restraints weight = 4172.410| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.52 r_work: 0.2741 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3386 Z= 0.144 Angle : 0.436 5.505 4598 Z= 0.229 Chirality : 0.041 0.126 501 Planarity : 0.004 0.046 586 Dihedral : 4.676 45.638 462 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.59 % Allowed : 17.99 % Favored : 81.42 % 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: 1.62 (0.43), residues: 414 helix: 2.37 (0.35), residues: 210 sheet: 0.28 (0.66), residues: 73 loop : -0.59 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.002 0.001 HIS A 267 PHE 0.011 0.001 PHE A 341 TYR 0.009 0.001 TYR A 363 ARG 0.009 0.000 ARG A 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2014.85 seconds wall clock time: 37 minutes 7.74 seconds (2227.74 seconds total)