Starting phenix.real_space_refine on Thu Jul 18 19:38:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgu_50428/07_2024/9fgu_50428.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgu_50428/07_2024/9fgu_50428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgu_50428/07_2024/9fgu_50428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgu_50428/07_2024/9fgu_50428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgu_50428/07_2024/9fgu_50428.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgu_50428/07_2024/9fgu_50428.cif" } resolution = 4.3 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= -0.004 sd= 0.035 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 13 5.16 5 C 2071 2.51 5 N 545 2.21 5 O 612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 405": "OD1" <-> "OD2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3241 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1541 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 11, 'TRANS': 179} Chain: "E" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1686 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain breaks: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.34, per 1000 atoms: 1.03 Number of scatterers: 3241 At special positions: 0 Unit cell: (80.01, 64.897, 92.456, 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 13 16.00 O 612 8.00 N 545 7.00 C 2071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 222 " 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 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 576.8 milliseconds 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 11.6% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.889A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.641A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 479 through 483 removed outlier: 3.836A pdb=" N GLY C 482 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.633A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.860A pdb=" N TYR E 79 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.949A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG E 97 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE E 107 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.949A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.509A pdb=" N CYS E 156 " --> pdb=" O PHE E 205 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR E 208 " --> pdb=" O SER E 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 144 through 145 removed outlier: 6.289A pdb=" N LEU E 144 " --> pdb=" O GLU E 240 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE E 219 " --> pdb=" O GLN E 172 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR E 221 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR E 170 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU E 167 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE E 182 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TRP E 169 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU E 180 " --> pdb=" O TRP E 169 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN E 171 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS E 173 " --> pdb=" O GLN E 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 144 through 145 removed outlier: 6.289A pdb=" N LEU E 144 " --> pdb=" O GLU E 240 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU E 224 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR E 232 " --> pdb=" O GLU E 224 " (cutoff:3.500A) 84 hydrogen bonds defined for protein. 204 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: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1037 1.34 - 1.46: 864 1.46 - 1.58: 1409 1.58 - 1.70: 0 1.70 - 1.81: 15 Bond restraints: 3325 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.68e+00 bond pdb=" CB ASP C 428 " pdb=" CG ASP C 428 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.46e+00 bond pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.24e+00 bond pdb=" CA ASP C 428 " pdb=" CB ASP C 428 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.33e-02 5.65e+03 1.14e+00 bond pdb=" C3 NAG C1301 " pdb=" O3 NAG C1301 " ideal model delta sigma weight residual 1.403 1.422 -0.019 2.00e-02 2.50e+03 9.39e-01 ... (remaining 3320 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.31: 90 106.31 - 113.23: 1699 113.23 - 120.14: 1158 120.14 - 127.05: 1538 127.05 - 133.96: 35 Bond angle restraints: 4520 Sorted by residual: angle pdb=" N GLY C 431 " pdb=" CA GLY C 431 " pdb=" C GLY C 431 " ideal model delta sigma weight residual 112.04 106.92 5.12 1.02e+00 9.61e-01 2.52e+01 angle pdb=" CA GLY C 431 " pdb=" C GLY C 431 " pdb=" O GLY C 431 " ideal model delta sigma weight residual 122.45 118.86 3.59 7.20e-01 1.93e+00 2.49e+01 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 108.38 114.61 -6.23 1.35e+00 5.49e-01 2.13e+01 angle pdb=" CA GLY C 431 " pdb=" C GLY C 431 " pdb=" N CYS C 432 " ideal model delta sigma weight residual 114.29 119.03 -4.74 1.41e+00 5.03e-01 1.13e+01 angle pdb=" N ALA E 218 " pdb=" CA ALA E 218 " pdb=" C ALA E 218 " ideal model delta sigma weight residual 107.88 112.26 -4.38 1.41e+00 5.03e-01 9.64e+00 ... (remaining 4515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 1762 17.27 - 34.54: 162 34.54 - 51.81: 25 51.81 - 69.07: 9 69.07 - 86.34: 6 Dihedral angle restraints: 1964 sinusoidal: 773 harmonic: 1191 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -149.47 63.47 1 1.00e+01 1.00e-02 5.31e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual -86.00 -26.72 -59.28 1 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" CA CYS C 379 " pdb=" C CYS C 379 " pdb=" N TYR C 380 " pdb=" CA TYR C 380 " ideal model delta harmonic sigma weight residual -180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 1961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 299 0.033 - 0.066: 115 0.066 - 0.098: 43 0.098 - 0.131: 30 0.131 - 0.164: 1 Chirality restraints: 488 Sorted by residual: chirality pdb=" CG LEU E 85 " pdb=" CB LEU E 85 " pdb=" CD1 LEU E 85 " pdb=" CD2 LEU E 85 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA ILE C 434 " pdb=" N ILE C 434 " pdb=" C ILE C 434 " pdb=" CB ILE C 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA ASP C 428 " pdb=" N ASP C 428 " pdb=" C ASP C 428 " pdb=" CB ASP C 428 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 485 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 478 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO C 479 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 479 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 479 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 108 " 0.008 2.00e-02 2.50e+03 9.29e-03 2.16e+00 pdb=" CG TRP E 108 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP E 108 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP E 108 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 108 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 108 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 108 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 108 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 108 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP E 108 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 192 " -0.020 5.00e-02 4.00e+02 2.95e-02 1.40e+00 pdb=" N PRO E 193 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO E 193 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 193 " -0.016 5.00e-02 4.00e+02 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 87 2.68 - 3.23: 3289 3.23 - 3.79: 4956 3.79 - 4.34: 6344 4.34 - 4.90: 9980 Nonbonded interactions: 24656 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.123 2.440 nonbonded pdb=" OG1 THR E 90 " pdb=" O VAL E 114 " model vdw 2.202 2.440 nonbonded pdb=" O TRP C 353 " pdb=" NH2 ARG C 466 " model vdw 2.205 2.520 nonbonded pdb=" NE2 GLN E 39 " pdb=" O LYS E 43 " model vdw 2.252 2.520 nonbonded pdb=" NH1 ARG E 211 " pdb=" O LEU E 212 " model vdw 2.260 2.520 ... (remaining 24651 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.250 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 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 : 0.003 0.033 3325 Z= 0.216 Angle : 0.715 6.419 4520 Z= 0.407 Chirality : 0.045 0.164 488 Planarity : 0.004 0.047 585 Dihedral : 13.955 86.342 1195 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.29 % Allowed : 0.86 % Favored : 98.85 % 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: -1.32 (0.40), residues: 407 helix: -1.17 (1.14), residues: 20 sheet: -0.09 (0.51), residues: 111 loop : -1.25 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 108 HIS 0.001 0.001 HIS C 519 PHE 0.019 0.002 PHE E 58 TYR 0.009 0.001 TYR C 365 ARG 0.003 0.000 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.366 Fit side-chains REVERT: E 238 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7604 (ttm110) outliers start: 1 outliers final: 1 residues processed: 66 average time/residue: 0.1925 time to fit residues: 14.9645 Evaluate side-chains 38 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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: 0.8980 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.0030 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS E 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3325 Z= 0.190 Angle : 0.658 6.798 4520 Z= 0.340 Chirality : 0.046 0.165 488 Planarity : 0.004 0.039 585 Dihedral : 6.501 59.950 480 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % 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: -1.18 (0.41), residues: 407 helix: -1.21 (1.02), residues: 27 sheet: -0.14 (0.50), residues: 114 loop : -1.05 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 169 HIS 0.002 0.001 HIS C 505 PHE 0.014 0.001 PHE C 392 TYR 0.014 0.001 TYR C 489 ARG 0.003 0.001 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: C 471 GLU cc_start: 0.6279 (pm20) cc_final: 0.5762 (pm20) REVERT: E 238 ARG cc_start: 0.7454 (mmm-85) cc_final: 0.7112 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1974 time to fit residues: 14.1969 Evaluate side-chains 40 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 0.0570 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN C 505 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3325 Z= 0.264 Angle : 0.717 6.955 4520 Z= 0.368 Chirality : 0.047 0.183 488 Planarity : 0.004 0.037 585 Dihedral : 6.844 59.604 480 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % 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: -1.57 (0.41), residues: 407 helix: -1.46 (1.20), residues: 20 sheet: -0.58 (0.46), residues: 131 loop : -1.28 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 169 HIS 0.004 0.002 HIS C 505 PHE 0.020 0.002 PHE C 392 TYR 0.011 0.002 TYR C 501 ARG 0.003 0.001 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: C 408 ARG cc_start: 0.9089 (tmm160) cc_final: 0.8751 (tmm160) REVERT: C 465 GLU cc_start: 0.8605 (tp30) cc_final: 0.8288 (tp30) REVERT: E 47 TRP cc_start: 0.8760 (t60) cc_final: 0.8470 (t60) REVERT: E 238 ARG cc_start: 0.7550 (mmm-85) cc_final: 0.7167 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2295 time to fit residues: 15.6400 Evaluate side-chains 41 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 3325 Z= 0.506 Angle : 0.930 11.265 4520 Z= 0.482 Chirality : 0.055 0.381 488 Planarity : 0.006 0.041 585 Dihedral : 8.000 59.574 480 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 34.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 0.29 % Allowed : 7.78 % Favored : 91.93 % 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: -1.93 (0.40), residues: 407 helix: -2.18 (1.10), residues: 20 sheet: -0.85 (0.52), residues: 109 loop : -1.45 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 353 HIS 0.002 0.001 HIS C 519 PHE 0.034 0.003 PHE C 392 TYR 0.027 0.003 TYR C 449 ARG 0.006 0.001 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: C 444 LYS cc_start: 0.6066 (ttpt) cc_final: 0.5792 (ttpt) REVERT: C 465 GLU cc_start: 0.8759 (tp30) cc_final: 0.8334 (tp30) REVERT: C 478 LYS cc_start: 0.8132 (tptm) cc_final: 0.7549 (tttt) REVERT: E 64 LYS cc_start: 0.9072 (mmmt) cc_final: 0.8589 (mmmt) outliers start: 1 outliers final: 1 residues processed: 55 average time/residue: 0.2139 time to fit residues: 13.8435 Evaluate side-chains 37 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3325 Z= 0.243 Angle : 0.744 9.673 4520 Z= 0.370 Chirality : 0.049 0.267 488 Planarity : 0.005 0.053 585 Dihedral : 7.032 59.134 480 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % 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: -1.73 (0.42), residues: 407 helix: -2.04 (1.16), residues: 20 sheet: -0.89 (0.47), residues: 127 loop : -1.21 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP E 169 HIS 0.001 0.000 HIS C 519 PHE 0.022 0.002 PHE C 392 TYR 0.017 0.001 TYR C 380 ARG 0.004 0.000 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.306 Fit side-chains REVERT: C 478 LYS cc_start: 0.7922 (tptm) cc_final: 0.7309 (tmtt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1986 time to fit residues: 13.2206 Evaluate side-chains 43 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3325 Z= 0.215 Angle : 0.723 9.796 4520 Z= 0.360 Chirality : 0.048 0.234 488 Planarity : 0.005 0.052 585 Dihedral : 6.732 59.566 480 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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: -1.59 (0.42), residues: 407 helix: -0.72 (1.25), residues: 21 sheet: -0.89 (0.47), residues: 123 loop : -1.18 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 108 HIS 0.001 0.000 HIS C 519 PHE 0.021 0.002 PHE C 392 TYR 0.014 0.001 TYR C 380 ARG 0.004 0.000 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.368 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1842 time to fit residues: 11.9489 Evaluate side-chains 41 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3325 Z= 0.222 Angle : 0.729 8.591 4520 Z= 0.363 Chirality : 0.048 0.223 488 Planarity : 0.005 0.050 585 Dihedral : 6.708 58.943 480 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: -1.54 (0.42), residues: 407 helix: -0.80 (1.23), residues: 21 sheet: -0.78 (0.47), residues: 123 loop : -1.18 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 108 HIS 0.001 0.000 HIS C 505 PHE 0.022 0.001 PHE C 392 TYR 0.012 0.001 TYR C 380 ARG 0.004 0.000 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.370 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1784 time to fit residues: 11.2404 Evaluate side-chains 39 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.0470 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 0.0050 chunk 28 optimal weight: 0.9990 overall best weight: 0.4692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3325 Z= 0.180 Angle : 0.702 9.449 4520 Z= 0.344 Chirality : 0.047 0.206 488 Planarity : 0.004 0.047 585 Dihedral : 6.372 58.159 480 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % 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: -1.20 (0.43), residues: 407 helix: -0.45 (1.49), residues: 14 sheet: -0.48 (0.50), residues: 115 loop : -0.97 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 108 HIS 0.000 0.000 HIS C 505 PHE 0.017 0.001 PHE E 58 TYR 0.010 0.001 TYR C 380 ARG 0.002 0.000 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.368 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1716 time to fit residues: 10.4817 Evaluate side-chains 38 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 0.0470 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 0.0170 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3325 Z= 0.195 Angle : 0.689 7.883 4520 Z= 0.343 Chirality : 0.047 0.193 488 Planarity : 0.004 0.042 585 Dihedral : 6.401 57.939 480 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -1.34 (0.42), residues: 407 helix: -1.69 (1.12), residues: 20 sheet: -0.56 (0.47), residues: 128 loop : -0.98 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 169 HIS 0.001 0.000 HIS C 505 PHE 0.020 0.001 PHE C 392 TYR 0.011 0.001 TYR C 380 ARG 0.003 0.000 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.408 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1740 time to fit residues: 10.4180 Evaluate side-chains 38 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 0.0570 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3325 Z= 0.169 Angle : 0.670 7.647 4520 Z= 0.332 Chirality : 0.047 0.186 488 Planarity : 0.004 0.040 585 Dihedral : 6.158 57.644 480 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -1.16 (0.42), residues: 407 helix: -0.20 (1.47), residues: 14 sheet: -0.36 (0.50), residues: 115 loop : -1.01 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 169 HIS 0.000 0.000 HIS C 505 PHE 0.017 0.001 PHE E 58 TYR 0.010 0.001 TYR C 380 ARG 0.003 0.000 ARG E 195 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.375 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1711 time to fit residues: 9.9799 Evaluate side-chains 38 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 40 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 39 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 = 0.3769 r_free = 0.3769 target = 0.105424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.094589 restraints weight = 12579.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.096921 restraints weight = 7766.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.098495 restraints weight = 5313.037| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3325 Z= 0.187 Angle : 0.672 7.549 4520 Z= 0.335 Chirality : 0.046 0.184 488 Planarity : 0.004 0.039 585 Dihedral : 6.263 57.980 480 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % 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: -1.32 (0.42), residues: 407 helix: -1.75 (1.09), residues: 20 sheet: -0.54 (0.47), residues: 128 loop : -0.98 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 169 HIS 0.000 0.000 HIS C 519 PHE 0.012 0.001 PHE C 347 TYR 0.010 0.001 TYR C 380 ARG 0.003 0.000 ARG E 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1300.82 seconds wall clock time: 24 minutes 17.40 seconds (1457.40 seconds total)