Starting phenix.real_space_refine on Wed Mar 5 18:49:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgu_50428/03_2025/9fgu_50428.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgu_50428/03_2025/9fgu_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/cci-nas-00/data/ceres_data/9fgu_50428/03_2025/9fgu_50428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgu_50428/03_2025/9fgu_50428.map" model { file = "/net/cci-nas-00/data/ceres_data/9fgu_50428/03_2025/9fgu_50428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgu_50428/03_2025/9fgu_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. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.10, per 1000 atoms: 1.27 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 429.6 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: 0.59 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: 0.93 Time building geometry restraints manager: 0.99 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: 0.00 - 1.28: 4226 1.28 - 2.57: 231 2.57 - 3.85: 49 3.85 - 5.13: 8 5.13 - 6.42: 6 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 3.040 nonbonded pdb=" OG1 THR E 90 " pdb=" O VAL E 114 " model vdw 2.202 3.040 nonbonded pdb=" O TRP C 353 " pdb=" NH2 ARG C 466 " model vdw 2.205 3.120 nonbonded pdb=" NE2 GLN E 39 " pdb=" O LYS E 43 " model vdw 2.252 3.120 nonbonded pdb=" NH1 ARG E 211 " pdb=" O LEU E 212 " model vdw 2.260 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 9.900 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.430 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.354 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: 0.2371 time to fit residues: 18.5777 Evaluate side-chains 38 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.0070 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.107653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.096219 restraints weight = 11828.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.098661 restraints weight = 7403.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.100347 restraints weight = 5078.421| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3325 Z= 0.205 Angle : 0.696 8.673 4520 Z= 0.359 Chirality : 0.047 0.162 488 Planarity : 0.005 0.040 585 Dihedral : 6.581 59.681 480 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % 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: -1.19 (0.41), residues: 407 helix: -0.51 (1.23), residues: 21 sheet: -0.16 (0.50), residues: 114 loop : -1.13 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 169 HIS 0.002 0.001 HIS C 505 PHE 0.014 0.002 PHE C 392 TYR 0.015 0.001 TYR C 489 ARG 0.004 0.001 ARG E 19 *********************** 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 to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: E 238 ARG cc_start: 0.7367 (mmm-85) cc_final: 0.7074 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2025 time to fit residues: 14.3577 Evaluate side-chains 39 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.105709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.094757 restraints weight = 12567.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.097063 restraints weight = 7803.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.098665 restraints weight = 5333.886| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2655 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= 0.221 Angle : 0.705 8.501 4520 Z= 0.358 Chirality : 0.047 0.161 488 Planarity : 0.004 0.036 585 Dihedral : 6.606 59.956 480 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % 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: -1.45 (0.41), residues: 407 helix: -1.12 (1.05), residues: 27 sheet: -0.53 (0.47), residues: 129 loop : -1.19 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 169 HIS 0.002 0.001 HIS C 505 PHE 0.019 0.001 PHE C 392 TYR 0.011 0.001 TYR C 508 ARG 0.004 0.001 ARG E 19 *********************** 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 58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.341 Fit side-chains REVERT: C 408 ARG cc_start: 0.9060 (tmm160) cc_final: 0.8728 (tmm160) REVERT: C 465 GLU cc_start: 0.8534 (tp30) cc_final: 0.8211 (tp30) REVERT: E 238 ARG cc_start: 0.7319 (mmm-85) cc_final: 0.7051 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2207 time to fit residues: 14.8600 Evaluate side-chains 41 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 0.0970 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN C 414 GLN C 505 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.107477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.096411 restraints weight = 12742.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.098765 restraints weight = 7822.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.100428 restraints weight = 5314.419| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3325 Z= 0.175 Angle : 0.662 7.122 4520 Z= 0.331 Chirality : 0.046 0.166 488 Planarity : 0.004 0.035 585 Dihedral : 6.257 58.807 480 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % 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: -1.16 (1.04), residues: 27 sheet: -0.36 (0.50), residues: 117 loop : -1.13 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 169 HIS 0.001 0.000 HIS C 505 PHE 0.016 0.001 PHE E 58 TYR 0.009 0.001 TYR C 508 ARG 0.003 0.000 ARG E 19 *********************** 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 58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.392 Fit side-chains REVERT: C 408 ARG cc_start: 0.9013 (tmm160) cc_final: 0.8773 (tmm160) REVERT: C 444 LYS cc_start: 0.6235 (ttpt) cc_final: 0.5965 (ttpt) REVERT: E 47 TRP cc_start: 0.8705 (t60) cc_final: 0.8477 (t60) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1921 time to fit residues: 13.1659 Evaluate side-chains 41 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.0040 chunk 1 optimal weight: 0.0770 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.3750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.107914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.096640 restraints weight = 12461.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.099135 restraints weight = 7551.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.100842 restraints weight = 5093.806| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3325 Z= 0.164 Angle : 0.655 7.233 4520 Z= 0.324 Chirality : 0.046 0.153 488 Planarity : 0.004 0.036 585 Dihedral : 6.097 58.172 480 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % 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: -1.35 (0.42), residues: 407 helix: -1.19 (1.02), residues: 27 sheet: -0.44 (0.50), residues: 117 loop : -1.10 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 169 HIS 0.000 0.000 HIS C 505 PHE 0.015 0.001 PHE E 58 TYR 0.008 0.001 TYR C 508 ARG 0.002 0.000 ARG E 19 *********************** 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 58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.340 Fit side-chains REVERT: C 444 LYS cc_start: 0.6246 (ttpt) cc_final: 0.6018 (ttpt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1936 time to fit residues: 13.2870 Evaluate side-chains 41 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.106109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.095213 restraints weight = 12921.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.097548 restraints weight = 7885.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.099116 restraints weight = 5356.699| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3325 Z= 0.199 Angle : 0.682 7.988 4520 Z= 0.346 Chirality : 0.046 0.183 488 Planarity : 0.004 0.035 585 Dihedral : 6.209 59.079 480 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % 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: -1.42 (0.42), residues: 407 helix: -0.55 (1.20), residues: 21 sheet: -0.60 (0.46), residues: 132 loop : -1.17 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP E 169 HIS 0.004 0.002 HIS C 505 PHE 0.017 0.001 PHE C 392 TYR 0.007 0.001 TYR E 183 ARG 0.003 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 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.380 Fit side-chains REVERT: C 444 LYS cc_start: 0.6246 (ttpt) cc_final: 0.5983 (ttpt) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2010 time to fit residues: 13.5949 Evaluate side-chains 38 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.0870 chunk 26 optimal weight: 0.0010 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 overall best weight: 0.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.108652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.097706 restraints weight = 12608.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.100041 restraints weight = 7788.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.101598 restraints weight = 5331.246| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.3989 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= 0.165 Angle : 0.665 8.084 4520 Z= 0.331 Chirality : 0.045 0.158 488 Planarity : 0.004 0.034 585 Dihedral : 5.919 57.908 480 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: -1.27 (0.42), residues: 407 helix: -0.40 (1.18), residues: 21 sheet: -0.52 (0.46), residues: 131 loop : -1.05 (0.40), residues: 255 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 0.018 0.001 PHE E 58 TYR 0.008 0.001 TYR C 508 ARG 0.002 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 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.359 Fit side-chains REVERT: C 444 LYS cc_start: 0.6256 (ttpt) cc_final: 0.6005 (ttpt) REVERT: E 38 ARG cc_start: 0.7924 (ptt180) cc_final: 0.7433 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1776 time to fit residues: 12.0017 Evaluate side-chains 38 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.104918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.093789 restraints weight = 12672.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.096133 restraints weight = 7800.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.097802 restraints weight = 5324.094| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3325 Z= 0.224 Angle : 0.695 8.189 4520 Z= 0.347 Chirality : 0.046 0.182 488 Planarity : 0.004 0.036 585 Dihedral : 6.204 57.054 480 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % 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: -1.65 (0.41), residues: 407 helix: -2.46 (0.80), residues: 27 sheet: -0.63 (0.47), residues: 128 loop : -1.19 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E 169 HIS 0.002 0.001 HIS C 505 PHE 0.020 0.001 PHE C 392 TYR 0.010 0.001 TYR C 449 ARG 0.003 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 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.398 Fit side-chains REVERT: C 444 LYS cc_start: 0.6242 (ttpt) cc_final: 0.5962 (ttpt) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2127 time to fit residues: 12.8343 Evaluate side-chains 36 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.105568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.094526 restraints weight = 12914.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.096887 restraints weight = 8020.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.098532 restraints weight = 5478.670| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.4198 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= 0.194 Angle : 0.681 7.727 4520 Z= 0.338 Chirality : 0.046 0.174 488 Planarity : 0.005 0.037 585 Dihedral : 6.169 57.895 480 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -2.05 (0.91), residues: 28 sheet: -0.62 (0.47), residues: 127 loop : -1.10 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 169 HIS 0.011 0.004 HIS C 505 PHE 0.019 0.001 PHE E 58 TYR 0.008 0.001 TYR E 183 ARG 0.006 0.000 ARG C 454 *********************** 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 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: C 444 LYS cc_start: 0.6262 (ttpt) cc_final: 0.6028 (ttpt) REVERT: C 453 TYR cc_start: 0.7379 (p90) cc_final: 0.7136 (p90) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1894 time to fit residues: 11.9740 Evaluate side-chains 38 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.0010 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 35 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.106923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.095819 restraints weight = 12454.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.098210 restraints weight = 7701.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.099865 restraints weight = 5265.716| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3325 Z= 0.175 Angle : 0.656 6.821 4520 Z= 0.326 Chirality : 0.046 0.165 488 Planarity : 0.004 0.038 585 Dihedral : 6.029 57.263 480 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % 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: -1.50 (0.42), residues: 407 helix: -2.04 (0.90), residues: 28 sheet: -0.58 (0.46), residues: 131 loop : -1.08 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 169 HIS 0.000 0.000 HIS C 505 PHE 0.013 0.001 PHE C 392 TYR 0.007 0.001 TYR E 183 ARG 0.007 0.000 ARG C 454 ********************** 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 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: C 444 LYS cc_start: 0.6263 (ttpt) cc_final: 0.6036 (ttpt) REVERT: C 453 TYR cc_start: 0.7273 (p90) cc_final: 0.7053 (p90) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1948 time to fit residues: 12.0845 Evaluate side-chains 38 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.105065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.093848 restraints weight = 12482.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.096304 restraints weight = 7583.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.098031 restraints weight = 5134.486| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3325 Z= 0.208 Angle : 0.672 7.537 4520 Z= 0.337 Chirality : 0.046 0.159 488 Planarity : 0.005 0.039 585 Dihedral : 6.223 57.663 480 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.46 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: -1.54 (0.42), residues: 407 helix: -1.99 (0.91), residues: 28 sheet: -0.61 (0.48), residues: 125 loop : -1.12 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP E 169 HIS 0.010 0.003 HIS C 505 PHE 0.018 0.002 PHE C 392 TYR 0.009 0.001 TYR E 183 ARG 0.005 0.000 ARG C 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1636.65 seconds wall clock time: 29 minutes 13.12 seconds (1753.12 seconds total)