Starting phenix.real_space_refine on Thu Nov 14 01:17:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgs_50420/11_2024/9fgs_50420.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgs_50420/11_2024/9fgs_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgs_50420/11_2024/9fgs_50420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgs_50420/11_2024/9fgs_50420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgs_50420/11_2024/9fgs_50420.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgs_50420/11_2024/9fgs_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 3.26, per 1000 atoms: 1.02 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: 0.64 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.38 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: 0.80 Time building geometry restraints manager: 0.77 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.930 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.910 ------------------------------------------------------------------------------- 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 : 0.348 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: 0.1546 time to fit residues: 12.1662 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 : 0.378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 368 LEU cc_start: 0.8687 (mm) cc_final: 0.8260 (mt) REVERT: E 75 LYS cc_start: 0.7541 (mmtt) cc_final: 0.7055 (tptm) outliers start: 7 outliers final: 4 residues processed: 56 average time/residue: 0.1577 time to fit residues: 10.9015 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 : 0.283 ------------------------------------------------------------------------------- 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 20 optimal weight: 0.0170 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 0.0370 chunk 12 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3263 Z= 0.164 Angle : 0.556 4.667 4440 Z= 0.288 Chirality : 0.042 0.129 489 Planarity : 0.004 0.038 573 Dihedral : 6.322 52.764 476 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 1.46 % Allowed : 12.28 % 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: -1.62 (0.41), residues: 404 helix: -4.60 (0.65), residues: 12 sheet: -0.21 (0.48), residues: 123 loop : -1.40 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 353 HIS 0.002 0.001 HIS C 519 PHE 0.012 0.001 PHE C 429 TYR 0.013 0.001 TYR C 380 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 61 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 368 LEU cc_start: 0.8599 (mm) cc_final: 0.8256 (mt) REVERT: C 405 ASP cc_start: 0.8547 (t0) cc_final: 0.8341 (t0) REVERT: E 75 LYS cc_start: 0.7568 (mmtt) cc_final: 0.7001 (tptm) outliers start: 5 outliers final: 5 residues processed: 59 average time/residue: 0.1418 time to fit residues: 10.5040 Evaluate side-chains 50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 342 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.0270 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3263 Z= 0.201 Angle : 0.581 4.757 4440 Z= 0.300 Chirality : 0.043 0.132 489 Planarity : 0.004 0.038 573 Dihedral : 7.004 59.900 476 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 2.92 % Allowed : 15.79 % Favored : 81.29 % 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: -1.78 (0.40), residues: 404 helix: -4.68 (0.57), residues: 12 sheet: -0.33 (0.48), residues: 125 loop : -1.50 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 353 HIS 0.003 0.002 HIS C 519 PHE 0.009 0.001 PHE C 374 TYR 0.013 0.001 TYR C 380 ARG 0.002 0.000 ARG E 38 *********************** 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 58 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 342 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8256 (m-10) REVERT: C 405 ASP cc_start: 0.8575 (t0) cc_final: 0.8338 (t0) REVERT: E 75 LYS cc_start: 0.7614 (mmtt) cc_final: 0.7051 (tptm) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.1523 time to fit residues: 10.2011 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 : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 342 PHE 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 22 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 33 optimal weight: 0.0370 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.0050 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.3410 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2202 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= 0.154 Angle : 0.552 4.996 4440 Z= 0.286 Chirality : 0.042 0.164 489 Planarity : 0.004 0.040 573 Dihedral : 6.542 52.495 476 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.66 % Favored : 91.09 % Rotamer: Outliers : 2.92 % Allowed : 16.96 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.40), residues: 404 helix: -4.64 (0.58), residues: 12 sheet: -0.25 (0.48), residues: 125 loop : -1.46 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 47 HIS 0.002 0.001 HIS C 519 PHE 0.009 0.001 PHE C 429 TYR 0.011 0.001 TYR E 79 ARG 0.002 0.000 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 60 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 ASP cc_start: 0.8504 (t0) cc_final: 0.8244 (t0) REVERT: C 452 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8218 (pp) REVERT: E 75 LYS cc_start: 0.7574 (mmtt) cc_final: 0.7031 (tptm) REVERT: E 216 ASP cc_start: 0.7938 (p0) cc_final: 0.7725 (p0) outliers start: 10 outliers final: 8 residues processed: 55 average time/residue: 0.1513 time to fit residues: 10.3089 Evaluate side-chains 53 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS 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 234 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3263 Z= 0.195 Angle : 0.575 5.393 4440 Z= 0.298 Chirality : 0.043 0.170 489 Planarity : 0.004 0.043 573 Dihedral : 6.247 52.798 476 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.66 % Favored : 91.09 % Rotamer: Outliers : 2.63 % Allowed : 18.13 % Favored : 79.24 % 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: -1.84 (0.40), residues: 404 helix: -4.81 (0.45), residues: 12 sheet: -0.34 (0.46), residues: 134 loop : -1.60 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 353 HIS 0.003 0.002 HIS C 519 PHE 0.017 0.001 PHE C 374 TYR 0.011 0.001 TYR C 380 ARG 0.003 0.001 ARG C 408 *********************** 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 59 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 ASP cc_start: 0.8488 (t0) cc_final: 0.8271 (t0) REVERT: E 75 LYS cc_start: 0.7560 (mmtt) cc_final: 0.7011 (tptm) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.1714 time to fit residues: 11.5161 Evaluate side-chains 52 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 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 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 39 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 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 409 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3263 Z= 0.194 Angle : 0.594 5.304 4440 Z= 0.307 Chirality : 0.043 0.134 489 Planarity : 0.004 0.043 573 Dihedral : 5.983 52.540 476 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.17 % Favored : 91.58 % Rotamer: Outliers : 2.92 % Allowed : 19.30 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.41), residues: 404 helix: -4.88 (0.37), residues: 12 sheet: -0.19 (0.46), residues: 132 loop : -1.54 (0.37), residues: 260 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 0.015 0.001 PHE C 374 TYR 0.011 0.001 TYR E 79 ARG 0.010 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 56 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 ASP cc_start: 0.8475 (t0) cc_final: 0.8202 (t0) REVERT: E 75 LYS cc_start: 0.7629 (mmtt) cc_final: 0.7000 (tptm) outliers start: 10 outliers final: 9 residues processed: 52 average time/residue: 0.1613 time to fit residues: 10.3278 Evaluate side-chains 54 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3263 Z= 0.251 Angle : 0.624 5.688 4440 Z= 0.325 Chirality : 0.044 0.153 489 Planarity : 0.005 0.044 573 Dihedral : 6.121 51.223 476 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.92 % Favored : 91.83 % Rotamer: Outliers : 2.92 % Allowed : 19.59 % Favored : 77.49 % 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: -1.82 (0.40), residues: 404 helix: -4.82 (0.41), residues: 12 sheet: -0.17 (0.47), residues: 127 loop : -1.65 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.004 0.003 HIS C 519 PHE 0.017 0.002 PHE C 374 TYR 0.012 0.001 TYR C 380 ARG 0.005 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 60 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 ASP cc_start: 0.8474 (t0) cc_final: 0.8177 (t0) REVERT: E 75 LYS cc_start: 0.7677 (tmtt) cc_final: 0.7058 (tptm) outliers start: 10 outliers final: 9 residues processed: 56 average time/residue: 0.1420 time to fit residues: 10.0380 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 : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3263 Z= 0.208 Angle : 0.624 5.261 4440 Z= 0.326 Chirality : 0.044 0.174 489 Planarity : 0.004 0.044 573 Dihedral : 6.025 52.043 476 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.17 % Favored : 91.58 % 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: -1.82 (0.41), residues: 404 helix: -4.89 (0.32), residues: 12 sheet: -0.21 (0.46), residues: 132 loop : -1.64 (0.37), residues: 260 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 0.016 0.001 PHE C 374 TYR 0.012 0.001 TYR C 495 ARG 0.004 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 58 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 ASP cc_start: 0.8396 (t0) cc_final: 0.8095 (t0) REVERT: E 75 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7016 (tptm) outliers start: 12 outliers final: 8 residues processed: 53 average time/residue: 0.1579 time to fit residues: 10.4162 Evaluate side-chains 54 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 342 PHE 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 11 LEU Chi-restraints excluded: chain E residue 75 LYS 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 32 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 chunk 9 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.0270 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 0.0670 chunk 6 optimal weight: 1.9990 overall best weight: 0.2776 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3263 Z= 0.166 Angle : 0.591 5.034 4440 Z= 0.308 Chirality : 0.044 0.220 489 Planarity : 0.005 0.044 573 Dihedral : 5.830 53.305 476 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.18 % Favored : 92.57 % Rotamer: Outliers : 2.63 % Allowed : 21.05 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.41), residues: 404 helix: -4.90 (0.32), residues: 12 sheet: -0.07 (0.48), residues: 126 loop : -1.48 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 353 HIS 0.002 0.001 HIS C 519 PHE 0.013 0.001 PHE C 400 TYR 0.011 0.001 TYR E 79 ARG 0.004 0.000 ARG E 195 ********************** 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 57 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 405 ASP cc_start: 0.8337 (t0) cc_final: 0.8035 (t0) REVERT: E 75 LYS cc_start: 0.7441 (tmtt) cc_final: 0.6913 (tptm) outliers start: 9 outliers final: 7 residues processed: 53 average time/residue: 0.1621 time to fit residues: 10.6459 Evaluate side-chains 51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 519 HIS Chi-restraints excluded: chain E residue 11 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 28 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.113919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102000 restraints weight = 7314.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.104225 restraints weight = 4436.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.105696 restraints weight = 3035.253| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3263 Z= 0.206 Angle : 0.614 7.578 4440 Z= 0.319 Chirality : 0.044 0.208 489 Planarity : 0.004 0.046 573 Dihedral : 5.810 52.212 476 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.66 % Favored : 91.09 % Rotamer: Outliers : 2.63 % Allowed : 21.64 % Favored : 75.73 % 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: -1.64 (0.41), residues: 404 helix: -4.90 (0.31), residues: 12 sheet: -0.09 (0.48), residues: 126 loop : -1.47 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.003 0.002 HIS C 519 PHE 0.012 0.001 PHE C 374 TYR 0.042 0.002 TYR C 473 ARG 0.004 0.001 ARG E 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1298.36 seconds wall clock time: 24 minutes 22.75 seconds (1462.75 seconds total)