Starting phenix.real_space_refine on Mon Feb 10 22:56:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgs_50420/02_2025/9fgs_50420.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgs_50420/02_2025/9fgs_50420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fgs_50420/02_2025/9fgs_50420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgs_50420/02_2025/9fgs_50420.map" model { file = "/net/cci-nas-00/data/ceres_data/9fgs_50420/02_2025/9fgs_50420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgs_50420/02_2025/9fgs_50420.cif" } resolution = 4.0 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= -0.003 sd= 0.047 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 14 5.16 5 C 2025 2.51 5 N 532 2.21 5 O 616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3187 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1513 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 11, 'TRANS': 178} Chain breaks: 1 Chain: "E" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1660 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 8, 'TRANS': 213} 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: 3.45, per 1000 atoms: 1.08 Number of scatterers: 3187 At special positions: 0 Unit cell: (83.566, 63.119, 88.011, 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 14 16.00 O 616 8.00 N 532 7.00 C 2025 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 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=2.04 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: 0.69 Conformation dependent library (CDL) restraints added in 401.3 milliseconds 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 6 sheets defined 7.3% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'C' and resid 364 through 368 removed outlier: 4.472A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 4.192A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.640A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.801A pdb=" N THR E 90 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 217 removed outlier: 3.972A pdb=" N LEU E 217 " --> pdb=" O ALA E 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 355 through 358 removed outlier: 4.253A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (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 3 through 7 removed outlier: 3.591A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU E 18 " --> pdb=" O MET E 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.799A pdb=" N THR E 115 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL E 12 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL E 114 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA E 91 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL E 50 " --> pdb=" O PHE E 58 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 137 through 139 removed outlier: 3.539A pdb=" N ALA E 152 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR E 206 " --> pdb=" O SER E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 187 through 188 removed outlier: 7.038A pdb=" N TRP E 169 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR E 183 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU E 167 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN E 223 " --> pdb=" O ALA E 168 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR E 236 " --> pdb=" O TYR E 220 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 165 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: 0.89 Time building geometry restraints manager: 0.85 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: 1021 1.34 - 1.46: 850 1.46 - 1.58: 1376 1.58 - 1.70: 0 1.70 - 1.81: 16 Bond restraints: 3263 Sorted by residual: bond pdb=" C ALA C 520 " pdb=" N PRO C 521 " ideal model delta sigma weight residual 1.332 1.356 -0.024 1.12e-02 7.97e+03 4.66e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.08e+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 9.26e-01 bond pdb=" CB GLU E 215 " pdb=" CG GLU E 215 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.94e-01 ... (remaining 3258 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 4074 1.04 - 2.08: 277 2.08 - 3.13: 61 3.13 - 4.17: 21 4.17 - 5.21: 7 Bond angle restraints: 4440 Sorted by residual: angle pdb=" CA ALA C 520 " pdb=" C ALA C 520 " pdb=" N PRO C 521 " ideal model delta sigma weight residual 117.67 120.55 -2.88 1.09e+00 8.42e-01 6.98e+00 angle pdb=" CA ARG E 211 " pdb=" CB ARG E 211 " pdb=" CG ARG E 211 " ideal model delta sigma weight residual 114.10 119.31 -5.21 2.00e+00 2.50e-01 6.79e+00 angle pdb=" CA ALA C 520 " pdb=" C ALA C 520 " pdb=" O ALA C 520 " ideal model delta sigma weight residual 121.08 118.83 2.25 8.90e-01 1.26e+00 6.38e+00 angle pdb=" N ALA E 91 " pdb=" CA ALA E 91 " pdb=" C ALA E 91 " ideal model delta sigma weight residual 107.73 111.65 -3.92 1.61e+00 3.86e-01 5.92e+00 angle pdb=" N SER C 438 " pdb=" CA SER C 438 " pdb=" C SER C 438 " ideal model delta sigma weight residual 108.17 112.64 -4.47 1.85e+00 2.92e-01 5.83e+00 ... (remaining 4435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 1747 17.91 - 35.82: 153 35.82 - 53.73: 22 53.73 - 71.64: 6 71.64 - 89.55: 2 Dihedral angle restraints: 1930 sinusoidal: 744 harmonic: 1186 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 152.82 -59.82 1 1.00e+01 1.00e-02 4.77e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 128.68 -35.68 1 1.00e+01 1.00e-02 1.80e+01 dihedral pdb=" CB CYS E 156 " pdb=" SG CYS E 156 " pdb=" SG CYS E 222 " pdb=" CB CYS E 222 " ideal model delta sinusoidal sigma weight residual 93.00 59.90 33.10 1 1.00e+01 1.00e-02 1.56e+01 ... (remaining 1927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 373 0.044 - 0.087: 87 0.087 - 0.131: 28 0.131 - 0.175: 0 0.175 - 0.218: 1 Chirality restraints: 489 Sorted by residual: chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA VAL C 401 " pdb=" N VAL C 401 " pdb=" C VAL C 401 " pdb=" CB VAL C 401 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ASP E 216 " pdb=" N ASP E 216 " pdb=" C ASP E 216 " pdb=" CB ASP E 216 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 486 not shown) Planarity restraints: 574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " 0.001 2.00e-02 2.50e+03 1.93e-02 4.66e+00 pdb=" CG ASN C 343 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " -0.019 2.00e-02 2.50e+03 pdb=" C1 NAG C1301 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 336 " 0.026 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO C 337 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 383 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO C 384 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 384 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 384 " -0.022 5.00e-02 4.00e+02 ... (remaining 571 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 716 2.78 - 3.31: 2841 3.31 - 3.84: 4747 3.84 - 4.37: 5344 4.37 - 4.90: 9350 Nonbonded interactions: 22998 Sorted by model distance: nonbonded pdb=" OD2 ASP C 442 " pdb=" OH TYR C 451 " model vdw 2.251 3.040 nonbonded pdb=" OD1 ASP C 427 " pdb=" N ASP C 428 " model vdw 2.290 3.120 nonbonded pdb=" OG SER C 349 " pdb=" O LEU C 452 " model vdw 2.294 3.040 nonbonded pdb=" O SER C 359 " pdb=" OG1 THR C 523 " model vdw 2.313 3.040 nonbonded pdb=" NH1 ARG E 38 " pdb=" OD1 ASP E 89 " model vdw 2.319 3.120 ... (remaining 22993 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: 3.680 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.420 Find NCS groups from input model: 0.060 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 0.036 3263 Z= 0.201 Angle : 0.657 5.212 4440 Z= 0.360 Chirality : 0.043 0.218 489 Planarity : 0.004 0.041 573 Dihedral : 13.377 89.545 1162 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % 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: -1.99 (0.39), residues: 404 helix: -4.31 (0.76), residues: 12 sheet: -0.72 (0.47), residues: 124 loop : -1.53 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 436 HIS 0.001 0.001 HIS C 519 PHE 0.019 0.002 PHE C 392 TYR 0.016 0.001 TYR C 473 ARG 0.004 0.001 ARG E 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.385 Fit side-chains REVERT: C 368 LEU cc_start: 0.8618 (mm) cc_final: 0.8229 (mt) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1782 time to fit residues: 13.8261 Evaluate side-chains 45 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 20 optimal weight: 0.1980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 172 GLN E 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.103068 restraints weight = 7495.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.105134 restraints weight = 4516.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.106499 restraints weight = 3084.909| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3263 Z= 0.207 Angle : 0.612 6.177 4440 Z= 0.313 Chirality : 0.043 0.135 489 Planarity : 0.004 0.038 573 Dihedral : 6.828 57.467 476 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.05 % Allowed : 9.65 % Favored : 88.30 % 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: -1.83 (0.40), residues: 404 helix: -4.56 (0.68), residues: 12 sheet: -0.53 (0.45), residues: 134 loop : -1.47 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 353 HIS 0.001 0.001 HIS C 519 PHE 0.018 0.002 PHE C 429 TYR 0.017 0.001 TYR C 380 ARG 0.002 0.001 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 368 LEU cc_start: 0.8692 (mm) cc_final: 0.8265 (mt) REVERT: E 75 LYS cc_start: 0.7563 (mmtt) cc_final: 0.7044 (tptm) outliers start: 7 outliers final: 4 residues processed: 56 average time/residue: 0.1414 time to fit residues: 9.8988 Evaluate side-chains 50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 234 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 0.0470 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.0020 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.0470 chunk 36 optimal weight: 0.0050 overall best weight: 0.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106865 restraints weight = 7266.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109273 restraints weight = 4177.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110887 restraints weight = 2740.537| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3263 Z= 0.136 Angle : 0.541 4.744 4440 Z= 0.279 Chirality : 0.042 0.131 489 Planarity : 0.004 0.037 573 Dihedral : 6.114 54.087 476 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.17 % Allowed : 12.57 % Favored : 86.26 % 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: -1.55 (0.41), residues: 404 helix: -4.64 (0.62), residues: 12 sheet: -0.14 (0.48), residues: 123 loop : -1.35 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 47 HIS 0.001 0.001 HIS C 519 PHE 0.014 0.001 PHE C 429 TYR 0.011 0.001 TYR E 79 ARG 0.002 0.000 ARG E 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 368 LEU cc_start: 0.8609 (mm) cc_final: 0.8307 (mt) REVERT: C 405 ASP cc_start: 0.8693 (t0) cc_final: 0.8442 (t0) REVERT: E 75 LYS cc_start: 0.7423 (mmtt) cc_final: 0.6965 (tptm) outliers start: 4 outliers final: 4 residues processed: 58 average time/residue: 0.1514 time to fit residues: 10.7877 Evaluate side-chains 50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 234 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN C 506 GLN E 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.104405 restraints weight = 7290.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.106500 restraints weight = 4411.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.107990 restraints weight = 3026.310| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3263 Z= 0.178 Angle : 0.554 4.572 4440 Z= 0.284 Chirality : 0.042 0.129 489 Planarity : 0.004 0.038 573 Dihedral : 6.629 56.460 476 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.63 % Allowed : 15.50 % Favored : 81.87 % 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: -1.61 (0.41), residues: 404 helix: -4.53 (0.68), residues: 12 sheet: -0.22 (0.48), residues: 125 loop : -1.38 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 353 HIS 0.003 0.002 HIS C 519 PHE 0.009 0.001 PHE C 429 TYR 0.012 0.001 TYR C 380 ARG 0.002 0.000 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 368 LEU cc_start: 0.8634 (mm) cc_final: 0.8202 (mt) REVERT: C 405 ASP cc_start: 0.8646 (t0) cc_final: 0.8378 (t0) REVERT: E 75 LYS cc_start: 0.7667 (mmtt) cc_final: 0.7061 (tptm) outliers start: 9 outliers final: 5 residues processed: 56 average time/residue: 0.1444 time to fit residues: 9.9806 Evaluate side-chains 53 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 234 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN E 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.113942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102268 restraints weight = 7372.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104376 restraints weight = 4504.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.105879 restraints weight = 3100.135| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3263 Z= 0.223 Angle : 0.580 4.758 4440 Z= 0.300 Chirality : 0.043 0.146 489 Planarity : 0.004 0.036 573 Dihedral : 6.499 51.212 476 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.66 % Favored : 91.09 % Rotamer: Outliers : 2.63 % Allowed : 16.37 % Favored : 80.99 % 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: -1.80 (0.40), residues: 404 helix: -4.54 (0.69), residues: 12 sheet: -0.36 (0.47), residues: 127 loop : -1.52 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 353 HIS 0.004 0.002 HIS C 519 PHE 0.013 0.001 PHE C 374 TYR 0.013 0.001 TYR C 380 ARG 0.002 0.001 ARG E 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 ASP cc_start: 0.8644 (t0) cc_final: 0.8430 (t0) REVERT: E 75 LYS cc_start: 0.7709 (mmtt) cc_final: 0.7084 (tptm) REVERT: E 216 ASP cc_start: 0.8011 (p0) cc_final: 0.7807 (p0) outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 0.1710 time to fit residues: 11.1666 Evaluate side-chains 53 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 234 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 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 409 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101616 restraints weight = 7467.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.103897 restraints weight = 4475.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105377 restraints weight = 3036.135| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3263 Z= 0.215 Angle : 0.578 4.686 4440 Z= 0.300 Chirality : 0.043 0.135 489 Planarity : 0.004 0.036 573 Dihedral : 6.203 52.228 476 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.91 % Favored : 90.84 % Rotamer: Outliers : 3.22 % Allowed : 17.84 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.41), residues: 404 helix: -4.56 (0.69), residues: 12 sheet: -0.31 (0.48), residues: 125 loop : -1.44 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.003 0.002 HIS C 519 PHE 0.009 0.001 PHE C 374 TYR 0.012 0.001 TYR C 380 ARG 0.002 0.001 ARG E 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 ASP cc_start: 0.8638 (t0) cc_final: 0.8363 (t0) REVERT: C 452 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8194 (pp) REVERT: E 75 LYS cc_start: 0.7645 (mmtt) cc_final: 0.7035 (tptm) outliers start: 11 outliers final: 7 residues processed: 56 average time/residue: 0.1531 time to fit residues: 10.6582 Evaluate side-chains 54 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 234 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.100212 restraints weight = 7458.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.102464 restraints weight = 4506.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.104035 restraints weight = 3072.561| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3263 Z= 0.243 Angle : 0.619 5.843 4440 Z= 0.321 Chirality : 0.043 0.135 489 Planarity : 0.004 0.036 573 Dihedral : 6.115 51.652 476 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.91 % Favored : 90.84 % Rotamer: Outliers : 3.22 % Allowed : 17.84 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.41), residues: 404 helix: -4.52 (0.71), residues: 12 sheet: -0.13 (0.48), residues: 125 loop : -1.44 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.002 HIS C 519 PHE 0.011 0.001 PHE E 196 TYR 0.011 0.001 TYR C 380 ARG 0.009 0.001 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 ASP cc_start: 0.8576 (t0) cc_final: 0.8272 (t0) REVERT: C 452 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8207 (pp) REVERT: E 75 LYS cc_start: 0.7747 (mmtt) cc_final: 0.7036 (tptm) outliers start: 11 outliers final: 8 residues processed: 59 average time/residue: 0.1563 time to fit residues: 11.2921 Evaluate side-chains 56 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 234 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 0.0970 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.113375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.101043 restraints weight = 7288.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.103294 restraints weight = 4454.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.104812 restraints weight = 3058.129| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3263 Z= 0.225 Angle : 0.626 5.339 4440 Z= 0.327 Chirality : 0.044 0.177 489 Planarity : 0.005 0.040 573 Dihedral : 6.073 52.043 476 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.92 % Favored : 91.83 % Rotamer: Outliers : 3.22 % Allowed : 19.88 % Favored : 76.90 % 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: -1.70 (0.41), residues: 404 helix: -4.58 (0.67), residues: 12 sheet: -0.22 (0.48), residues: 126 loop : -1.49 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.003 0.002 HIS C 519 PHE 0.007 0.001 PHE E 196 TYR 0.011 0.001 TYR C 380 ARG 0.009 0.001 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 ASP cc_start: 0.8555 (t0) cc_final: 0.8242 (t0) REVERT: C 452 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8217 (pp) REVERT: E 75 LYS cc_start: 0.7635 (tmtt) cc_final: 0.7039 (tptm) outliers start: 11 outliers final: 10 residues processed: 54 average time/residue: 0.1592 time to fit residues: 10.5676 Evaluate side-chains 56 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 234 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.112330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.099807 restraints weight = 7411.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.102049 restraints weight = 4513.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.103575 restraints weight = 3102.354| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3263 Z= 0.260 Angle : 0.643 5.719 4440 Z= 0.338 Chirality : 0.044 0.173 489 Planarity : 0.004 0.033 573 Dihedral : 6.131 51.554 476 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.16 % Favored : 90.59 % Rotamer: Outliers : 3.80 % Allowed : 19.59 % Favored : 76.61 % 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: -1.76 (0.41), residues: 404 helix: -4.65 (0.60), residues: 12 sheet: -0.22 (0.48), residues: 125 loop : -1.55 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.002 HIS C 519 PHE 0.011 0.001 PHE C 400 TYR 0.011 0.001 TYR C 380 ARG 0.005 0.001 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 ASP cc_start: 0.8562 (t0) cc_final: 0.8233 (t0) REVERT: C 452 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8232 (pp) REVERT: E 75 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7046 (tptm) REVERT: E 213 GLU cc_start: 0.7912 (pm20) cc_final: 0.7712 (pm20) outliers start: 13 outliers final: 10 residues processed: 52 average time/residue: 0.1720 time to fit residues: 10.8886 Evaluate side-chains 55 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 234 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN E 6 GLN E 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.112508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.100128 restraints weight = 7426.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102361 restraints weight = 4524.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.103865 restraints weight = 3115.237| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3263 Z= 0.233 Angle : 0.642 5.825 4440 Z= 0.336 Chirality : 0.044 0.154 489 Planarity : 0.005 0.045 573 Dihedral : 6.095 51.923 476 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.66 % Favored : 91.09 % Rotamer: Outliers : 3.51 % Allowed : 19.59 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.41), residues: 404 helix: -4.67 (0.59), residues: 12 sheet: -0.23 (0.48), residues: 125 loop : -1.58 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.002 HIS C 519 PHE 0.006 0.001 PHE E 196 TYR 0.012 0.001 TYR C 495 ARG 0.003 0.001 ARG E 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 ASP cc_start: 0.8537 (t0) cc_final: 0.8210 (t0) REVERT: C 452 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8243 (pp) REVERT: E 75 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7003 (tptm) outliers start: 12 outliers final: 9 residues processed: 51 average time/residue: 0.1576 time to fit residues: 9.8359 Evaluate side-chains 55 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 234 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 20 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN E 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.101842 restraints weight = 7513.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104128 restraints weight = 4546.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.105614 restraints weight = 3095.226| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3263 Z= 0.190 Angle : 0.609 5.509 4440 Z= 0.319 Chirality : 0.044 0.161 489 Planarity : 0.004 0.033 573 Dihedral : 5.895 52.722 476 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.66 % Favored : 91.09 % Rotamer: Outliers : 3.51 % Allowed : 20.47 % Favored : 76.02 % 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: -1.76 (0.41), residues: 404 helix: -4.66 (0.59), residues: 12 sheet: -0.23 (0.48), residues: 126 loop : -1.54 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 353 HIS 0.002 0.001 HIS C 519 PHE 0.012 0.001 PHE C 400 TYR 0.011 0.001 TYR E 79 ARG 0.003 0.001 ARG E 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1476.80 seconds wall clock time: 27 minutes 12.81 seconds (1632.81 seconds total)