Starting phenix.real_space_refine on Sun Mar 10 18:31:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9a_24253/03_2024/7n9a_24253.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9a_24253/03_2024/7n9a_24253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9a_24253/03_2024/7n9a_24253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9a_24253/03_2024/7n9a_24253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9a_24253/03_2024/7n9a_24253.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9a_24253/03_2024/7n9a_24253.pdb" } resolution = 3.5 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= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1545 atoms to isotropic. 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 11 5.16 5 C 1540 2.51 5 N 420 2.21 5 O 460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2431 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 886 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "E" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1545 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Time building chain proxies: 1.86, per 1000 atoms: 0.77 Number of scatterers: 2431 At special positions: 0 Unit cell: (79.68, 60.59, 79.68, 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 11 16.00 O 460 8.00 N 420 7.00 C 1540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 94 " distance=2.05 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 443.8 milliseconds 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 5 sheets defined 13.5% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.524A pdb=" N THR A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.580A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 371 removed outlier: 4.099A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 390 removed outlier: 3.817A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 408 removed outlier: 4.382A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 405 through 408' Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.544A pdb=" N SER A 7 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 67 " --> pdb=" O GLN A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.786A pdb=" N VAL A 113 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 90 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 91 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG A 36 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 45 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.786A pdb=" N VAL A 113 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 90 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.597A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 66 hydrogen bonds defined for protein. 171 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: 0.58 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 796 1.34 - 1.47: 657 1.47 - 1.59: 1025 1.59 - 1.71: 0 1.71 - 1.84: 12 Bond restraints: 2490 Sorted by residual: bond pdb=" N PRO E 499 " pdb=" CD PRO E 499 " ideal model delta sigma weight residual 1.473 1.446 0.027 1.40e-02 5.10e+03 3.76e+00 bond pdb=" CB VAL A 2 " pdb=" CG1 VAL A 2 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.78e+00 bond pdb=" CA PRO E 499 " pdb=" CB PRO E 499 " ideal model delta sigma weight residual 1.534 1.558 -0.024 1.49e-02 4.50e+03 2.65e+00 bond pdb=" CG LEU E 518 " pdb=" CD1 LEU E 518 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" CB PHE A 45 " pdb=" CG PHE A 45 " ideal model delta sigma weight residual 1.502 1.467 0.035 2.30e-02 1.89e+03 2.36e+00 ... (remaining 2485 not shown) Histogram of bond angle deviations from ideal: 95.67 - 103.33: 27 103.33 - 110.99: 803 110.99 - 118.65: 1063 118.65 - 126.30: 1455 126.30 - 133.96: 33 Bond angle restraints: 3381 Sorted by residual: angle pdb=" CA PRO E 499 " pdb=" N PRO E 499 " pdb=" CD PRO E 499 " ideal model delta sigma weight residual 112.00 102.71 9.29 1.40e+00 5.10e-01 4.40e+01 angle pdb=" N GLY E 482 " pdb=" CA GLY E 482 " pdb=" C GLY E 482 " ideal model delta sigma weight residual 114.90 122.64 -7.74 1.54e+00 4.22e-01 2.53e+01 angle pdb=" CA CYS A 22 " pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " ideal model delta sigma weight residual 114.40 125.79 -11.39 2.30e+00 1.89e-01 2.45e+01 angle pdb=" C GLN E 409 " pdb=" N ILE E 410 " pdb=" CA ILE E 410 " ideal model delta sigma weight residual 123.11 117.10 6.01 1.36e+00 5.41e-01 1.95e+01 angle pdb=" CA TYR E 495 " pdb=" CB TYR E 495 " pdb=" CG TYR E 495 " ideal model delta sigma weight residual 113.90 121.76 -7.86 1.80e+00 3.09e-01 1.91e+01 ... (remaining 3376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 1342 16.68 - 33.36: 93 33.36 - 50.04: 20 50.04 - 66.72: 5 66.72 - 83.40: 4 Dihedral angle restraints: 1464 sinusoidal: 569 harmonic: 895 Sorted by residual: dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 94 " pdb=" CB CYS A 94 " ideal model delta sinusoidal sigma weight residual 93.00 165.21 -72.21 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 145.12 -52.12 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" SG CYS E 391 " pdb=" CB CYS E 525 " pdb=" SG CYS E 525 " pdb=" CA CYS E 525 " ideal model delta sinusoidal sigma weight residual -73.00 -14.99 -58.01 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 1461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 202 0.045 - 0.090: 101 0.090 - 0.136: 39 0.136 - 0.181: 12 0.181 - 0.226: 4 Chirality restraints: 358 Sorted by residual: chirality pdb=" CA ASN E 481 " pdb=" N ASN E 481 " pdb=" C ASN E 481 " pdb=" CB ASN E 481 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA PHE E 497 " pdb=" N PHE E 497 " pdb=" C PHE E 497 " pdb=" CB PHE E 497 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CG LEU E 455 " pdb=" CB LEU E 455 " pdb=" CD1 LEU E 455 " pdb=" CD2 LEU E 455 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 355 not shown) Planarity restraints: 445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 498 " 0.067 5.00e-02 4.00e+02 9.57e-02 1.46e+01 pdb=" N PRO E 499 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO E 499 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 499 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 495 " -0.026 2.00e-02 2.50e+03 2.25e-02 1.01e+01 pdb=" CG TYR E 495 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR E 495 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR E 495 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 495 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 495 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR E 495 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 495 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 497 " 0.003 2.00e-02 2.50e+03 2.34e-02 9.60e+00 pdb=" CG PHE E 497 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE E 497 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE E 497 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE E 497 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 PHE E 497 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE E 497 " 0.000 2.00e-02 2.50e+03 ... (remaining 442 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 75 2.69 - 3.24: 2344 3.24 - 3.79: 3625 3.79 - 4.35: 4704 4.35 - 4.90: 7651 Nonbonded interactions: 18399 Sorted by model distance: nonbonded pdb=" O THR A 101 " pdb=" OH TYR E 489 " model vdw 2.135 2.440 nonbonded pdb=" OD1 ASN E 448 " pdb=" ND2 ASN E 450 " model vdw 2.182 2.520 nonbonded pdb=" O GLN E 414 " pdb=" NZ LYS E 424 " model vdw 2.246 2.520 nonbonded pdb=" O ASN A 72 " pdb=" ND2 ASN A 72 " model vdw 2.315 2.520 nonbonded pdb=" OD1 ASN E 388 " pdb=" N ASP E 389 " model vdw 2.316 2.520 ... (remaining 18394 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 5.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 25.770 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.490 Find NCS groups from input model: 0.070 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 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 : 0.007 0.055 2490 Z= 0.446 Angle : 1.259 11.386 3381 Z= 0.734 Chirality : 0.064 0.226 358 Planarity : 0.007 0.096 445 Dihedral : 12.630 83.395 885 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: -0.16 (0.45), residues: 308 helix: -2.13 (0.71), residues: 30 sheet: 1.69 (0.55), residues: 74 loop : -0.48 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP E 353 HIS 0.005 0.002 HIS A 30 PHE 0.042 0.004 PHE E 497 TYR 0.056 0.005 TYR E 495 ARG 0.006 0.001 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.233 Fit side-chains REVERT: A 42 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6715 (tm-30) REVERT: E 489 TYR cc_start: 0.6940 (m-80) cc_final: 0.6408 (m-80) REVERT: E 501 ASN cc_start: 0.7721 (m110) cc_final: 0.7519 (m110) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1014 time to fit residues: 9.1531 Evaluate side-chains 66 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.0980 chunk 22 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.1980 chunk 8 optimal weight: 0.3980 overall best weight: 0.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2490 Z= 0.267 Angle : 0.679 6.596 3381 Z= 0.374 Chirality : 0.048 0.137 358 Planarity : 0.005 0.038 445 Dihedral : 5.559 22.911 349 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.33 % Allowed : 12.02 % Favored : 85.66 % 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: -0.37 (0.44), residues: 308 helix: -2.50 (0.71), residues: 31 sheet: 1.64 (0.56), residues: 79 loop : -0.68 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 107 HIS 0.002 0.001 HIS A 30 PHE 0.018 0.002 PHE E 497 TYR 0.020 0.002 TYR E 449 ARG 0.003 0.001 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.291 Fit side-chains REVERT: A 18 LEU cc_start: 0.7175 (tp) cc_final: 0.6970 (tp) REVERT: A 42 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6792 (tm-30) REVERT: E 489 TYR cc_start: 0.6983 (m-80) cc_final: 0.6534 (m-80) REVERT: E 501 ASN cc_start: 0.7765 (m110) cc_final: 0.7555 (m110) outliers start: 6 outliers final: 4 residues processed: 64 average time/residue: 0.1113 time to fit residues: 8.9132 Evaluate side-chains 64 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 29 optimal weight: 0.0050 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 14 optimal weight: 0.2980 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2490 Z= 0.223 Angle : 0.592 6.588 3381 Z= 0.322 Chirality : 0.045 0.143 358 Planarity : 0.005 0.040 445 Dihedral : 5.236 18.368 349 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.10 % Allowed : 13.18 % Favored : 83.72 % 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: -0.45 (0.45), residues: 308 helix: -2.60 (0.72), residues: 29 sheet: 1.15 (0.55), residues: 79 loop : -0.55 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 34 HIS 0.002 0.001 HIS A 30 PHE 0.034 0.002 PHE E 497 TYR 0.013 0.002 TYR E 449 ARG 0.002 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.269 Fit side-chains REVERT: A 42 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6875 (tm-30) REVERT: E 358 ILE cc_start: 0.7900 (mm) cc_final: 0.7620 (mt) outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 0.1098 time to fit residues: 8.8810 Evaluate side-chains 65 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.4980 chunk 13 optimal weight: 0.3980 chunk 18 optimal weight: 0.0770 chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.0010 chunk 0 optimal weight: 0.9990 overall best weight: 0.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2490 Z= 0.297 Angle : 0.641 10.157 3381 Z= 0.340 Chirality : 0.046 0.150 358 Planarity : 0.005 0.046 445 Dihedral : 5.408 18.543 349 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.04 % Allowed : 15.89 % Favored : 79.07 % 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: -0.72 (0.45), residues: 308 helix: -2.75 (0.75), residues: 29 sheet: 0.76 (0.55), residues: 79 loop : -0.64 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 107 HIS 0.003 0.001 HIS A 30 PHE 0.041 0.003 PHE E 497 TYR 0.017 0.002 TYR E 453 ARG 0.002 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.272 Fit side-chains REVERT: A 42 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6926 (tm-30) REVERT: E 395 VAL cc_start: 0.7768 (OUTLIER) cc_final: 0.7542 (t) outliers start: 13 outliers final: 11 residues processed: 73 average time/residue: 0.1121 time to fit residues: 10.2609 Evaluate side-chains 80 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.0980 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 17 optimal weight: 0.4980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2490 Z= 0.279 Angle : 0.612 6.285 3381 Z= 0.332 Chirality : 0.046 0.147 358 Planarity : 0.005 0.047 445 Dihedral : 5.358 19.253 349 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.43 % Allowed : 20.16 % Favored : 74.42 % 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: -1.03 (0.44), residues: 308 helix: -2.89 (0.76), residues: 31 sheet: 0.46 (0.56), residues: 79 loop : -0.80 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 34 HIS 0.003 0.001 HIS A 30 PHE 0.043 0.002 PHE E 497 TYR 0.016 0.002 TYR E 495 ARG 0.002 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.272 Fit side-chains REVERT: A 42 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6974 (tm-30) outliers start: 14 outliers final: 13 residues processed: 64 average time/residue: 0.1155 time to fit residues: 9.1324 Evaluate side-chains 74 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 501 ASN Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 0.0470 chunk 3 optimal weight: 0.1980 chunk 16 optimal weight: 0.0170 chunk 21 optimal weight: 0.1980 overall best weight: 0.1516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2490 Z= 0.184 Angle : 0.559 6.028 3381 Z= 0.299 Chirality : 0.044 0.151 358 Planarity : 0.005 0.047 445 Dihedral : 4.929 18.169 349 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 6.59 % Allowed : 18.60 % Favored : 74.81 % 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: -1.04 (0.44), residues: 308 helix: -2.89 (0.74), residues: 31 sheet: 0.43 (0.55), residues: 78 loop : -0.79 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 34 HIS 0.002 0.001 HIS A 30 PHE 0.031 0.002 PHE E 497 TYR 0.011 0.001 TYR E 495 ARG 0.002 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 0.297 Fit side-chains REVERT: A 42 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6954 (tm-30) REVERT: A 68 ILE cc_start: 0.6947 (mm) cc_final: 0.6590 (mm) REVERT: E 457 ARG cc_start: 0.8320 (ttt-90) cc_final: 0.7946 (ttt-90) outliers start: 17 outliers final: 11 residues processed: 74 average time/residue: 0.1179 time to fit residues: 10.7132 Evaluate side-chains 77 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 501 ASN Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.0010 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.0170 chunk 18 optimal weight: 0.0670 chunk 17 optimal weight: 0.1980 chunk 13 optimal weight: 0.3980 chunk 11 optimal weight: 0.1980 chunk 8 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 14 optimal weight: 0.2980 overall best weight: 0.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2490 Z= 0.176 Angle : 0.572 6.022 3381 Z= 0.300 Chirality : 0.044 0.136 358 Planarity : 0.005 0.048 445 Dihedral : 4.708 17.710 349 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.04 % Allowed : 21.71 % Favored : 73.26 % 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: -1.10 (0.44), residues: 308 helix: -3.14 (0.65), residues: 31 sheet: 0.39 (0.56), residues: 78 loop : -0.79 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 34 HIS 0.002 0.001 HIS A 30 PHE 0.033 0.002 PHE E 497 TYR 0.014 0.001 TYR E 495 ARG 0.002 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.282 Fit side-chains REVERT: A 42 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6962 (tm-30) REVERT: A 68 ILE cc_start: 0.6967 (mm) cc_final: 0.6654 (mm) REVERT: E 457 ARG cc_start: 0.8019 (ttt-90) cc_final: 0.7777 (ttt90) outliers start: 13 outliers final: 12 residues processed: 74 average time/residue: 0.1229 time to fit residues: 11.0864 Evaluate side-chains 80 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 27 optimal weight: 0.3980 chunk 25 optimal weight: 0.0970 chunk 16 optimal weight: 0.0980 chunk 11 optimal weight: 0.1980 chunk 21 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 overall best weight: 0.1778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2490 Z= 0.209 Angle : 0.594 7.668 3381 Z= 0.309 Chirality : 0.044 0.154 358 Planarity : 0.005 0.048 445 Dihedral : 4.772 18.884 349 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.81 % Allowed : 22.48 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.44), residues: 308 helix: -3.07 (0.69), residues: 31 sheet: 0.56 (0.57), residues: 79 loop : -0.86 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 107 HIS 0.002 0.001 HIS A 30 PHE 0.029 0.002 PHE E 497 TYR 0.009 0.001 TYR E 453 ARG 0.005 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 0.278 Fit side-chains REVERT: A 42 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6921 (tm-30) REVERT: A 68 ILE cc_start: 0.7054 (mm) cc_final: 0.6777 (mm) REVERT: E 457 ARG cc_start: 0.7952 (ttt-90) cc_final: 0.7735 (ttt90) outliers start: 15 outliers final: 12 residues processed: 75 average time/residue: 0.1269 time to fit residues: 11.4994 Evaluate side-chains 79 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 501 ASN Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 19 optimal weight: 0.3980 chunk 29 optimal weight: 0.0670 chunk 27 optimal weight: 0.0040 chunk 23 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.0040 chunk 14 optimal weight: 0.0470 chunk 25 optimal weight: 0.4980 overall best weight: 0.0640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2490 Z= 0.154 Angle : 0.611 10.718 3381 Z= 0.304 Chirality : 0.044 0.150 358 Planarity : 0.005 0.048 445 Dihedral : 4.469 17.286 349 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.26 % Allowed : 24.03 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.44), residues: 308 helix: -2.99 (0.73), residues: 31 sheet: 0.72 (0.57), residues: 78 loop : -0.84 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 34 HIS 0.001 0.001 HIS A 30 PHE 0.026 0.002 PHE E 497 TYR 0.008 0.001 TYR E 473 ARG 0.003 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.266 Fit side-chains REVERT: A 42 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6900 (tm-30) REVERT: A 68 ILE cc_start: 0.7017 (mm) cc_final: 0.6758 (mm) outliers start: 11 outliers final: 10 residues processed: 68 average time/residue: 0.1312 time to fit residues: 10.7626 Evaluate side-chains 75 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 359 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 6 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.0670 chunk 4 optimal weight: 0.1980 chunk 20 optimal weight: 0.0670 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.1834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2490 Z= 0.212 Angle : 0.621 9.825 3381 Z= 0.314 Chirality : 0.044 0.131 358 Planarity : 0.005 0.048 445 Dihedral : 4.691 17.674 349 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.65 % Allowed : 22.87 % Favored : 72.48 % 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: -0.98 (0.45), residues: 308 helix: -2.86 (0.75), residues: 31 sheet: 0.44 (0.56), residues: 84 loop : -0.76 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E 353 HIS 0.002 0.001 HIS A 30 PHE 0.030 0.002 PHE E 497 TYR 0.009 0.001 TYR E 453 ARG 0.005 0.000 ARG A 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.280 Fit side-chains REVERT: A 42 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6980 (tm-30) REVERT: A 68 ILE cc_start: 0.7062 (mm) cc_final: 0.6807 (mm) REVERT: E 374 PHE cc_start: 0.7271 (m-80) cc_final: 0.7044 (m-80) outliers start: 12 outliers final: 12 residues processed: 69 average time/residue: 0.1311 time to fit residues: 10.9403 Evaluate side-chains 76 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 501 ASN Chi-restraints excluded: chain E residue 518 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.0870 chunk 16 optimal weight: 0.0570 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.0670 chunk 18 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 0.0030 chunk 29 optimal weight: 0.1980 chunk 1 optimal weight: 0.2980 chunk 28 optimal weight: 0.0980 overall best weight: 0.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.147122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.134582 restraints weight = 4298.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.138479 restraints weight = 2328.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.141083 restraints weight = 1380.776| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2490 Z= 0.157 Angle : 0.613 9.666 3381 Z= 0.306 Chirality : 0.043 0.154 358 Planarity : 0.005 0.048 445 Dihedral : 4.347 16.372 349 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.88 % Allowed : 25.19 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.45), residues: 308 helix: -2.83 (0.78), residues: 31 sheet: 0.79 (0.56), residues: 79 loop : -0.78 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 353 HIS 0.001 0.001 HIS A 30 PHE 0.025 0.002 PHE E 497 TYR 0.009 0.001 TYR E 473 ARG 0.002 0.000 ARG A 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1533.20 seconds wall clock time: 28 minutes 3.54 seconds (1683.54 seconds total)