Starting phenix.real_space_refine on Mon Jan 13 16:42:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgu_50428/01_2025/9fgu_50428.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgu_50428/01_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_50428/01_2025/9fgu_50428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgu_50428/01_2025/9fgu_50428.map" model { file = "/net/cci-nas-00/data/ceres_data/9fgu_50428/01_2025/9fgu_50428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgu_50428/01_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-5571/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: 3.61, per 1000 atoms: 1.11 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: 1.08 Conformation dependent library (CDL) restraints added in 383.4 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: 0.43 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: 0.85 Time building geometry restraints manager: 0.89 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: 2.640 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.410 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.120 ------------------------------------------------------------------------------- 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 : 0.388 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: 0.2209 time to fit residues: 17.1007 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 : 0.383 ------------------------------------------------------------------------------- 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: 0.7980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 0.8980 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.108556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.097760 restraints weight = 12146.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.100014 restraints weight = 7787.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.101580 restraints weight = 5401.680| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2031 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 : 0.685 8.762 4520 Z= 0.351 Chirality : 0.047 0.164 488 Planarity : 0.004 0.039 585 Dihedral : 6.516 59.910 480 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 8.07 % 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: -1.17 (0.41), residues: 407 helix: -0.57 (1.20), residues: 21 sheet: -0.15 (0.50), residues: 114 loop : -1.11 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 169 HIS 0.002 0.001 HIS C 505 PHE 0.013 0.001 PHE C 392 TYR 0.014 0.001 TYR C 489 ARG 0.003 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 61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: C 471 GLU cc_start: 0.6411 (pm20) cc_final: 0.6052 (pm20) REVERT: E 238 ARG cc_start: 0.7310 (mmm-85) cc_final: 0.7065 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2085 time to fit residues: 14.9539 Evaluate side-chains 40 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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: 0.9980 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 0.0370 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.106736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.095723 restraints weight = 12173.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.098027 restraints weight = 7561.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.099592 restraints weight = 5194.677| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3325 Z= 0.201 Angle : 0.684 8.564 4520 Z= 0.346 Chirality : 0.046 0.157 488 Planarity : 0.004 0.036 585 Dihedral : 6.462 59.487 480 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % 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: -1.33 (0.41), residues: 407 helix: -1.28 (1.00), residues: 27 sheet: -0.31 (0.51), residues: 114 loop : -1.13 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 169 HIS 0.002 0.001 HIS C 505 PHE 0.014 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 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.337 Fit side-chains REVERT: C 444 LYS cc_start: 0.6460 (ttpt) cc_final: 0.6146 (ttpt) REVERT: E 47 TRP cc_start: 0.8659 (t60) cc_final: 0.8383 (t60) REVERT: E 230 ARG cc_start: 0.8270 (ptp-170) cc_final: 0.7949 (ptp-170) REVERT: E 238 ARG cc_start: 0.7273 (mmm-85) cc_final: 0.7032 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2150 time to fit residues: 14.3129 Evaluate side-chains 43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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: 0.3980 chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.103597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.092211 restraints weight = 12699.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.094643 restraints weight = 7721.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.096322 restraints weight = 5242.784| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3325 Z= 0.261 Angle : 0.726 7.502 4520 Z= 0.366 Chirality : 0.048 0.204 488 Planarity : 0.005 0.036 585 Dihedral : 6.722 59.804 480 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.41), residues: 407 helix: -1.26 (1.04), residues: 27 sheet: -0.47 (0.50), residues: 119 loop : -1.21 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP E 169 HIS 0.001 0.000 HIS C 519 PHE 0.016 0.002 PHE E 58 TYR 0.011 0.002 TYR E 79 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 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.375 Fit side-chains REVERT: C 465 GLU cc_start: 0.8568 (tp30) cc_final: 0.8237 (tp30) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2052 time to fit residues: 13.7990 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 : 0.438 ------------------------------------------------------------------------------- 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: 0.0170 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.0370 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 GLN ** 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 = 0.3782 r_free = 0.3782 target = 0.106765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.095690 restraints weight = 12488.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.098104 restraints weight = 7655.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.099712 restraints weight = 5192.004| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3414 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= 0.177 Angle : 0.667 6.704 4520 Z= 0.333 Chirality : 0.046 0.174 488 Planarity : 0.004 0.040 585 Dihedral : 6.287 58.651 480 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.41), residues: 407 helix: -1.25 (1.04), residues: 27 sheet: -0.49 (0.49), residues: 119 loop : -1.13 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 169 HIS 0.003 0.001 HIS C 505 PHE 0.017 0.001 PHE E 58 TYR 0.008 0.001 TYR C 508 ARG 0.003 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 59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.375 Fit side-chains REVERT: C 408 ARG cc_start: 0.9001 (tmm160) cc_final: 0.8774 (tmm160) REVERT: C 444 LYS cc_start: 0.6185 (ttpt) cc_final: 0.5938 (ttpt) REVERT: C 453 TYR cc_start: 0.7296 (p90) cc_final: 0.7086 (p90) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1944 time to fit residues: 13.6771 Evaluate side-chains 42 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 0.0170 chunk 3 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.106391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.094816 restraints weight = 12601.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.097396 restraints weight = 7513.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.099190 restraints weight = 5006.737| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3653 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= 0.185 Angle : 0.682 7.906 4520 Z= 0.338 Chirality : 0.046 0.182 488 Planarity : 0.004 0.039 585 Dihedral : 6.252 58.801 480 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.42), residues: 407 helix: -1.25 (1.04), residues: 27 sheet: -0.50 (0.49), residues: 119 loop : -1.08 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP E 169 HIS 0.001 0.001 HIS C 505 PHE 0.013 0.001 PHE C 347 TYR 0.006 0.001 TYR C 449 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 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.340 Fit side-chains REVERT: C 378 LYS cc_start: 0.8359 (pttp) cc_final: 0.7956 (tmmt) REVERT: C 444 LYS cc_start: 0.6283 (ttpt) cc_final: 0.5995 (ttpt) REVERT: C 453 TYR cc_start: 0.7396 (p90) cc_final: 0.7118 (p90) REVERT: C 465 GLU cc_start: 0.8598 (tp30) cc_final: 0.8386 (tp30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2107 time to fit residues: 14.0032 Evaluate side-chains 40 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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: 3.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 26 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.105039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.093852 restraints weight = 12313.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.096267 restraints weight = 7452.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.097923 restraints weight = 5019.219| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3325 Z= 0.211 Angle : 0.700 8.071 4520 Z= 0.349 Chirality : 0.046 0.195 488 Planarity : 0.004 0.042 585 Dihedral : 6.353 58.587 480 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: -1.44 (0.41), residues: 407 helix: -0.19 (1.27), residues: 21 sheet: -0.60 (0.46), residues: 130 loop : -1.23 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP E 169 HIS 0.002 0.001 HIS C 505 PHE 0.020 0.002 PHE C 392 TYR 0.009 0.001 TYR C 449 ARG 0.003 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 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.381 Fit side-chains REVERT: C 444 LYS cc_start: 0.6269 (ttpt) cc_final: 0.6033 (ttpt) REVERT: C 453 TYR cc_start: 0.7456 (p90) cc_final: 0.7139 (p90) REVERT: C 465 GLU cc_start: 0.8666 (tp30) cc_final: 0.8362 (tp30) REVERT: E 64 LYS cc_start: 0.9109 (mmmt) cc_final: 0.8896 (mmmt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2200 time to fit residues: 14.0364 Evaluate side-chains 40 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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: 3.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.105078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.094262 restraints weight = 12489.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.096611 restraints weight = 7697.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.098176 restraints weight = 5235.698| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3325 Z= 0.207 Angle : 0.693 7.851 4520 Z= 0.346 Chirality : 0.046 0.187 488 Planarity : 0.004 0.042 585 Dihedral : 6.325 58.262 480 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % 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: -0.24 (1.27), residues: 21 sheet: -0.74 (0.46), residues: 129 loop : -1.25 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 169 HIS 0.002 0.001 HIS C 505 PHE 0.017 0.001 PHE C 392 TYR 0.008 0.001 TYR C 449 ARG 0.004 0.001 ARG C 408 *********************** 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 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.349 Fit side-chains REVERT: C 444 LYS cc_start: 0.6274 (ttpt) cc_final: 0.6034 (ttpt) REVERT: C 453 TYR cc_start: 0.7446 (p90) cc_final: 0.7109 (p90) REVERT: C 465 GLU cc_start: 0.8660 (tp30) cc_final: 0.8458 (tp30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2072 time to fit residues: 12.9581 Evaluate side-chains 40 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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: 0.2980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.106310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.095641 restraints weight = 12681.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.098003 restraints weight = 7799.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.099594 restraints weight = 5271.870| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.4168 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= 0.188 Angle : 0.701 6.848 4520 Z= 0.349 Chirality : 0.046 0.171 488 Planarity : 0.004 0.040 585 Dihedral : 6.222 57.890 480 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % 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: -1.47 (0.42), residues: 407 helix: 0.20 (1.60), residues: 14 sheet: -0.71 (0.45), residues: 134 loop : -1.21 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 169 HIS 0.019 0.006 HIS C 505 PHE 0.017 0.001 PHE E 58 TYR 0.008 0.001 TYR C 508 ARG 0.004 0.000 ARG C 408 *********************** 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 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.372 Fit side-chains REVERT: C 444 LYS cc_start: 0.6283 (ttpt) cc_final: 0.6075 (ttpt) REVERT: C 453 TYR cc_start: 0.7443 (p90) cc_final: 0.7116 (p90) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2020 time to fit residues: 12.2373 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 : 0.391 ------------------------------------------------------------------------------- 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: 2.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 20 optimal weight: 0.0670 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 0.0870 chunk 38 optimal weight: 0.0980 chunk 35 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.1896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.109821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.098688 restraints weight = 12167.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.101162 restraints weight = 7375.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.102830 restraints weight = 4967.510| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.4328 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= 0.156 Angle : 0.664 6.904 4520 Z= 0.328 Chirality : 0.045 0.153 488 Planarity : 0.004 0.037 585 Dihedral : 5.872 57.466 480 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % 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: -1.32 (0.42), residues: 407 helix: -0.78 (1.34), residues: 16 sheet: -0.61 (0.47), residues: 127 loop : -1.02 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 47 HIS 0.003 0.001 HIS C 505 PHE 0.011 0.001 PHE E 217 TYR 0.007 0.001 TYR C 508 ARG 0.003 0.000 ARG C 408 ********************** 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 60 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: C 453 TYR cc_start: 0.7305 (p90) cc_final: 0.6995 (p90) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1941 time to fit residues: 13.8670 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 : 0.531 ------------------------------------------------------------------------------- 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: 0.0570 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.107037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.095655 restraints weight = 12120.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.098072 restraints weight = 7431.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.099725 restraints weight = 5067.432| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.4306 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= 0.194 Angle : 0.679 6.870 4520 Z= 0.339 Chirality : 0.046 0.163 488 Planarity : 0.004 0.035 585 Dihedral : 6.063 56.728 480 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % 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: -1.57 (0.42), residues: 407 helix: -2.65 (0.76), residues: 27 sheet: -0.54 (0.48), residues: 128 loop : -1.11 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 169 HIS 0.010 0.003 HIS C 505 PHE 0.015 0.001 PHE E 58 TYR 0.009 0.001 TYR C 449 ARG 0.003 0.000 ARG C 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1588.33 seconds wall clock time: 29 minutes 52.22 seconds (1792.22 seconds total)