Starting phenix.real_space_refine on Sun Mar 10 19:54:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1t_35932/03_2024/8j1t_35932.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1t_35932/03_2024/8j1t_35932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1t_35932/03_2024/8j1t_35932.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1t_35932/03_2024/8j1t_35932.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1t_35932/03_2024/8j1t_35932.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1t_35932/03_2024/8j1t_35932.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 1374 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 17 5.16 5 C 2035 2.51 5 N 543 2.21 5 O 609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3204 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 874 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "K" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "F" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1505 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 176} Chain breaks: 1 Time building chain proxies: 2.28, per 1000 atoms: 0.71 Number of scatterers: 3204 At special positions: 0 Unit cell: (63.05, 64.02, 92.15, 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 17 16.00 O 609 8.00 N 543 7.00 C 2035 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 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: 1.23 Conformation dependent library (CDL) restraints added in 593.1 milliseconds 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 10.2% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'H' and resid 29 through 33 removed outlier: 3.895A pdb=" N ASN H 33 " --> pdb=" O VAL H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.670A pdb=" N ARG H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 343 Processing helix chain 'F' and resid 366 through 372 removed outlier: 3.851A pdb=" N ASN F 370 " --> pdb=" O SER F 366 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE F 371 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 388 removed outlier: 4.094A pdb=" N ASN F 388 " --> pdb=" O THR F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.573A pdb=" N SER F 408 " --> pdb=" O ASN F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.632A pdb=" N TYR F 421 " --> pdb=" O ASN F 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.884A pdb=" N GLN H 4 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER H 22 " --> pdb=" O SER H 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.178A pdb=" N GLY H 11 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL H 114 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR H 34 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET H 35 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL H 51 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP H 37 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.932A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 45 through 48 removed outlier: 5.799A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 354 through 355 removed outlier: 3.585A pdb=" N ASN F 354 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER F 399 " --> pdb=" O ASN F 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'F' and resid 452 through 454 76 hydrogen bonds defined for protein. 183 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: 0.75 Time building geometry restraints manager: 1.30 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: 1029 1.34 - 1.46: 859 1.46 - 1.58: 1377 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 3287 Sorted by residual: bond pdb=" CA ILE K 29 " pdb=" CB ILE K 29 " ideal model delta sigma weight residual 1.553 1.538 0.015 7.40e-03 1.83e+04 4.28e+00 bond pdb=" CB ASN F 343 " pdb=" CG ASN F 343 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.63e+00 bond pdb=" CA ILE H 107 " pdb=" CB ILE H 107 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.03e+00 bond pdb=" CA VAL H 49 " pdb=" CB VAL H 49 " ideal model delta sigma weight residual 1.545 1.536 0.009 9.10e-03 1.21e+04 9.38e-01 bond pdb=" CB PHE F 400 " pdb=" CG PHE F 400 " ideal model delta sigma weight residual 1.502 1.480 0.022 2.30e-02 1.89e+03 8.92e-01 ... (remaining 3282 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.01: 102 107.01 - 113.75: 1707 113.75 - 120.48: 1234 120.48 - 127.22: 1390 127.22 - 133.96: 33 Bond angle restraints: 4466 Sorted by residual: angle pdb=" C GLN K 89 " pdb=" CA GLN K 89 " pdb=" CB GLN K 89 " ideal model delta sigma weight residual 111.17 106.80 4.37 1.96e+00 2.60e-01 4.98e+00 angle pdb=" C SER K 93 " pdb=" CA SER K 93 " pdb=" CB SER K 93 " ideal model delta sigma weight residual 111.71 106.94 4.77 2.23e+00 2.01e-01 4.58e+00 angle pdb=" CA ALA F 411 " pdb=" C ALA F 411 " pdb=" N PRO F 412 " ideal model delta sigma weight residual 117.62 119.65 -2.03 1.03e+00 9.43e-01 3.88e+00 angle pdb=" N GLN K 89 " pdb=" CA GLN K 89 " pdb=" CB GLN K 89 " ideal model delta sigma weight residual 111.46 114.42 -2.96 1.54e+00 4.22e-01 3.70e+00 angle pdb=" CA GLY K 28 " pdb=" C GLY K 28 " pdb=" O GLY K 28 " ideal model delta sigma weight residual 122.61 120.22 2.39 1.28e+00 6.10e-01 3.47e+00 ... (remaining 4461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 1761 15.68 - 31.35: 129 31.35 - 47.03: 31 47.03 - 62.70: 6 62.70 - 78.38: 3 Dihedral angle restraints: 1930 sinusoidal: 747 harmonic: 1183 Sorted by residual: dihedral pdb=" CB CYS F 480 " pdb=" SG CYS F 480 " pdb=" SG CYS F 488 " pdb=" CB CYS F 488 " ideal model delta sinusoidal sigma weight residual 93.00 171.38 -78.38 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CA ASN H 84 " pdb=" C ASN H 84 " pdb=" N SER H 85 " pdb=" CA SER H 85 " ideal model delta harmonic sigma weight residual -180.00 -151.42 -28.58 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CB CYS F 391 " pdb=" SG CYS F 391 " pdb=" SG CYS F 525 " pdb=" CB CYS F 525 " ideal model delta sinusoidal sigma weight residual 93.00 125.38 -32.38 1 1.00e+01 1.00e-02 1.49e+01 ... (remaining 1927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 288 0.034 - 0.067: 133 0.067 - 0.100: 32 0.100 - 0.134: 16 0.134 - 0.167: 5 Chirality restraints: 474 Sorted by residual: chirality pdb=" CA SER K 93 " pdb=" N SER K 93 " pdb=" C SER K 93 " pdb=" CB SER K 93 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.01e-01 chirality pdb=" CA VAL H 51 " pdb=" N VAL H 51 " pdb=" C VAL H 51 " pdb=" CB VAL H 51 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE F 402 " pdb=" N ILE F 402 " pdb=" C ILE F 402 " pdb=" CB ILE F 402 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 471 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 343 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C ASN F 343 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN F 343 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA F 344 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 396 " 0.011 2.00e-02 2.50e+03 7.76e-03 1.20e+00 pdb=" CG TYR F 396 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR F 396 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR F 396 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 396 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 396 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 396 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 396 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR H 53 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO H 54 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO H 54 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO H 54 " 0.015 5.00e-02 4.00e+02 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 469 2.76 - 3.29: 2996 3.29 - 3.83: 4905 3.83 - 4.36: 5946 4.36 - 4.90: 10335 Nonbonded interactions: 24651 Sorted by model distance: nonbonded pdb=" OH TYR K 36 " pdb=" OE1 GLN K 89 " model vdw 2.220 2.440 nonbonded pdb=" O GLN K 38 " pdb=" OG1 THR K 85 " model vdw 2.243 2.440 nonbonded pdb=" OE1 GLN K 6 " pdb=" OG1 THR K 104 " model vdw 2.266 2.440 nonbonded pdb=" O ASN F 439 " pdb=" OG SER F 443 " model vdw 2.339 2.440 nonbonded pdb=" OD1 ASN F 388 " pdb=" N ASP F 389 " model vdw 2.343 2.520 ... (remaining 24646 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 individual isotropic 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: 2.700 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: 0.000 Extract box with map and model: 11.080 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.110 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 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 : 0.004 0.032 3287 Z= 0.275 Angle : 0.585 5.169 4466 Z= 0.321 Chirality : 0.044 0.167 474 Planarity : 0.004 0.027 582 Dihedral : 11.734 66.984 1164 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.39), residues: 403 helix: -3.01 (0.65), residues: 33 sheet: -0.44 (0.47), residues: 134 loop : -1.47 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 353 HIS 0.005 0.001 HIS H 100 PHE 0.009 0.001 PHE F 338 TYR 0.018 0.002 TYR F 396 ARG 0.004 0.000 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: K 63 SER cc_start: 0.6549 (t) cc_final: 0.6239 (t) REVERT: F 453 TYR cc_start: 0.8207 (p90) cc_final: 0.7912 (p90) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1560 time to fit residues: 11.3091 Evaluate side-chains 58 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.0270 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 40 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 ASN ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3287 Z= 0.249 Angle : 0.565 5.255 4466 Z= 0.305 Chirality : 0.045 0.150 474 Planarity : 0.004 0.030 582 Dihedral : 5.089 39.989 458 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.86 % Allowed : 6.05 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.39), residues: 403 helix: -2.93 (0.69), residues: 33 sheet: -0.30 (0.50), residues: 120 loop : -1.48 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 436 HIS 0.005 0.001 HIS H 100 PHE 0.008 0.001 PHE F 338 TYR 0.013 0.001 TYR K 49 ARG 0.003 0.000 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: H 35 MET cc_start: 0.7353 (mmm) cc_final: 0.6872 (mtt) outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 0.1386 time to fit residues: 8.9756 Evaluate side-chains 54 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain F residue 393 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.0870 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 HIS ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 ASN F 417 ASN ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3287 Z= 0.275 Angle : 0.558 5.215 4466 Z= 0.300 Chirality : 0.045 0.152 474 Planarity : 0.004 0.031 582 Dihedral : 4.992 29.197 458 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.73 % Allowed : 8.65 % Favored : 89.63 % 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: -1.86 (0.39), residues: 403 helix: -2.94 (0.69), residues: 33 sheet: -0.45 (0.46), residues: 133 loop : -1.46 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 436 HIS 0.003 0.001 HIS H 100 PHE 0.013 0.002 PHE F 377 TYR 0.014 0.002 TYR F 423 ARG 0.004 0.000 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: H 101 SER cc_start: 0.8654 (p) cc_final: 0.8366 (p) outliers start: 6 outliers final: 6 residues processed: 54 average time/residue: 0.1380 time to fit residues: 9.4920 Evaluate side-chains 56 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain F residue 393 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 chunk 0 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: ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN F 354 ASN ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3287 Z= 0.275 Angle : 0.563 5.176 4466 Z= 0.300 Chirality : 0.045 0.153 474 Planarity : 0.003 0.031 582 Dihedral : 4.997 26.638 458 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.73 % Allowed : 10.37 % Favored : 87.90 % 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: -1.90 (0.39), residues: 403 helix: -3.01 (0.74), residues: 27 sheet: -0.39 (0.45), residues: 133 loop : -1.59 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 436 HIS 0.003 0.001 HIS H 100 PHE 0.008 0.001 PHE F 347 TYR 0.017 0.002 TYR F 423 ARG 0.003 0.000 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: H 101 SER cc_start: 0.8639 (p) cc_final: 0.8328 (p) outliers start: 6 outliers final: 6 residues processed: 53 average time/residue: 0.1385 time to fit residues: 9.3293 Evaluate side-chains 57 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 393 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.0370 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 ASN ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3287 Z= 0.292 Angle : 0.561 5.169 4466 Z= 0.301 Chirality : 0.045 0.152 474 Planarity : 0.003 0.031 582 Dihedral : 4.999 27.905 458 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.59 % Allowed : 10.95 % Favored : 86.46 % 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: -1.89 (0.39), residues: 403 helix: -2.94 (0.77), residues: 27 sheet: -0.34 (0.46), residues: 133 loop : -1.62 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 436 HIS 0.004 0.001 HIS H 100 PHE 0.008 0.002 PHE F 338 TYR 0.018 0.002 TYR F 423 ARG 0.002 0.000 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: H 101 SER cc_start: 0.8610 (p) cc_final: 0.8293 (p) REVERT: F 343 ASN cc_start: 0.8011 (t0) cc_final: 0.7706 (t0) REVERT: F 406 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7484 (tt0) outliers start: 9 outliers final: 7 residues processed: 57 average time/residue: 0.1325 time to fit residues: 9.6257 Evaluate side-chains 61 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 415 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 0.0570 chunk 27 optimal weight: 0.4980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 ASN F 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3287 Z= 0.214 Angle : 0.534 5.075 4466 Z= 0.286 Chirality : 0.045 0.153 474 Planarity : 0.003 0.031 582 Dihedral : 4.831 25.774 458 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.59 % Allowed : 10.37 % Favored : 87.03 % 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: -1.86 (0.39), residues: 403 helix: -2.93 (0.77), residues: 27 sheet: -0.31 (0.45), residues: 133 loop : -1.61 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 436 HIS 0.003 0.001 HIS H 100 PHE 0.009 0.001 PHE F 377 TYR 0.015 0.001 TYR F 423 ARG 0.002 0.000 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: H 101 SER cc_start: 0.8618 (p) cc_final: 0.8312 (p) REVERT: F 343 ASN cc_start: 0.8094 (t0) cc_final: 0.7718 (t0) REVERT: F 406 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7488 (tt0) outliers start: 9 outliers final: 8 residues processed: 57 average time/residue: 0.1506 time to fit residues: 10.6679 Evaluate side-chains 62 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 422 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 ASN F 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 3287 Z= 0.320 Angle : 0.572 5.717 4466 Z= 0.305 Chirality : 0.046 0.155 474 Planarity : 0.004 0.032 582 Dihedral : 4.995 27.750 458 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.46 % Allowed : 10.95 % Favored : 85.59 % 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: -1.94 (0.39), residues: 403 helix: -3.12 (0.73), residues: 27 sheet: -0.33 (0.46), residues: 133 loop : -1.68 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 436 HIS 0.003 0.001 HIS H 100 PHE 0.007 0.002 PHE F 375 TYR 0.017 0.002 TYR F 423 ARG 0.002 0.000 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: H 77 ASN cc_start: 0.7767 (t0) cc_final: 0.7423 (t0) REVERT: H 101 SER cc_start: 0.8595 (p) cc_final: 0.8273 (p) REVERT: F 343 ASN cc_start: 0.8121 (t0) cc_final: 0.7748 (t0) REVERT: F 406 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7491 (tt0) outliers start: 12 outliers final: 10 residues processed: 58 average time/residue: 0.1551 time to fit residues: 11.2628 Evaluate side-chains 63 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 422 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN F 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3287 Z= 0.245 Angle : 0.551 6.114 4466 Z= 0.295 Chirality : 0.045 0.152 474 Planarity : 0.003 0.031 582 Dihedral : 4.913 26.506 458 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.17 % Allowed : 11.82 % Favored : 85.01 % 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: -1.94 (0.39), residues: 403 helix: -3.11 (0.72), residues: 27 sheet: -0.28 (0.46), residues: 133 loop : -1.70 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 436 HIS 0.003 0.001 HIS H 100 PHE 0.008 0.001 PHE F 377 TYR 0.018 0.001 TYR F 423 ARG 0.002 0.000 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: H 77 ASN cc_start: 0.7739 (t0) cc_final: 0.7405 (t0) REVERT: H 101 SER cc_start: 0.8587 (p) cc_final: 0.8272 (p) REVERT: F 343 ASN cc_start: 0.8081 (t0) cc_final: 0.7703 (t0) REVERT: F 406 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7439 (tt0) outliers start: 11 outliers final: 10 residues processed: 57 average time/residue: 0.1565 time to fit residues: 11.1401 Evaluate side-chains 62 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 422 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 17 optimal weight: 0.0980 chunk 25 optimal weight: 0.0170 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 30 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 overall best weight: 0.1218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3287 Z= 0.138 Angle : 0.521 5.814 4466 Z= 0.274 Chirality : 0.044 0.150 474 Planarity : 0.003 0.030 582 Dihedral : 4.609 21.802 458 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.59 % Allowed : 12.39 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.39), residues: 403 helix: -2.97 (0.75), residues: 27 sheet: -0.13 (0.46), residues: 131 loop : -1.65 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 436 HIS 0.003 0.001 HIS H 100 PHE 0.013 0.001 PHE F 377 TYR 0.014 0.001 TYR F 423 ARG 0.002 0.000 ARG F 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: H 101 SER cc_start: 0.8592 (p) cc_final: 0.8295 (p) REVERT: F 343 ASN cc_start: 0.8125 (t0) cc_final: 0.7736 (t0) REVERT: F 406 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: F 422 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7792 (m110) outliers start: 9 outliers final: 6 residues processed: 58 average time/residue: 0.1488 time to fit residues: 10.6766 Evaluate side-chains 61 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 422 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3287 Z= 0.247 Angle : 0.544 5.515 4466 Z= 0.290 Chirality : 0.045 0.156 474 Planarity : 0.003 0.032 582 Dihedral : 4.698 24.490 458 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.31 % Allowed : 12.39 % Favored : 85.30 % 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: -1.87 (0.39), residues: 403 helix: -3.07 (0.73), residues: 27 sheet: -0.19 (0.46), residues: 131 loop : -1.69 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 436 HIS 0.005 0.001 HIS H 100 PHE 0.007 0.001 PHE F 375 TYR 0.014 0.001 TYR F 453 ARG 0.003 0.000 ARG F 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: H 101 SER cc_start: 0.8544 (p) cc_final: 0.8227 (p) REVERT: F 343 ASN cc_start: 0.8096 (t0) cc_final: 0.7713 (t0) REVERT: F 406 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7422 (tt0) outliers start: 8 outliers final: 7 residues processed: 54 average time/residue: 0.1626 time to fit residues: 10.8339 Evaluate side-chains 58 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 20 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 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 = 0.3797 r_free = 0.3797 target = 0.138856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.121698 restraints weight = 4491.233| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.21 r_work: 0.3462 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3287 Z= 0.269 Angle : 0.565 6.059 4466 Z= 0.300 Chirality : 0.045 0.156 474 Planarity : 0.004 0.032 582 Dihedral : 4.874 26.083 458 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.31 % Allowed : 13.26 % Favored : 84.44 % 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: -1.91 (0.39), residues: 403 helix: -3.06 (0.74), residues: 27 sheet: -0.24 (0.46), residues: 133 loop : -1.71 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 436 HIS 0.005 0.001 HIS H 100 PHE 0.007 0.001 PHE F 400 TYR 0.017 0.002 TYR F 423 ARG 0.003 0.000 ARG F 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1377.62 seconds wall clock time: 25 minutes 15.77 seconds (1515.77 seconds total)