Starting phenix.real_space_refine on Wed Nov 13 23:49:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c1u_45130/11_2024/9c1u_45130.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c1u_45130/11_2024/9c1u_45130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c1u_45130/11_2024/9c1u_45130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c1u_45130/11_2024/9c1u_45130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c1u_45130/11_2024/9c1u_45130.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c1u_45130/11_2024/9c1u_45130.cif" } resolution = 2.31 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1368 2.51 5 N 432 2.21 5 O 576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2376 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 198 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "B" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 198 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "C" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 198 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "D" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 198 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "E" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 198 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "F" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 198 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "G" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 198 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "H" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 198 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "I" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 198 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "J" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 198 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "K" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 198 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "L" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 198 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Time building chain proxies: 1.53, per 1000 atoms: 0.64 Number of scatterers: 2376 At special positions: 0 Unit cell: (62.25, 60.59, 48.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 576 8.00 N 432 7.00 C 1368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 268.3 milliseconds 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 43.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 372 through 378 removed outlier: 6.391A pdb=" N TYR A 372 " --> pdb=" O SER C 373 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE C 375 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER A 374 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU C 377 " --> pdb=" O SER A 374 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LYS A 376 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR C 372 " --> pdb=" O SER E 373 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE E 375 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N SER C 374 " --> pdb=" O ILE E 375 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU E 377 " --> pdb=" O SER C 374 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS C 376 " --> pdb=" O LEU E 377 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TYR E 372 " --> pdb=" O SER G 373 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE G 375 " --> pdb=" O TYR E 372 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SER E 374 " --> pdb=" O ILE G 375 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU G 377 " --> pdb=" O SER E 374 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS E 376 " --> pdb=" O LEU G 377 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR G 372 " --> pdb=" O SER I 373 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE I 375 " --> pdb=" O TYR G 372 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N SER G 374 " --> pdb=" O ILE I 375 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LEU I 377 " --> pdb=" O SER G 374 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LYS G 376 " --> pdb=" O LEU I 377 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR I 372 " --> pdb=" O SER K 373 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE K 375 " --> pdb=" O TYR I 372 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER I 374 " --> pdb=" O ILE K 375 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU K 377 " --> pdb=" O SER I 374 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LYS I 376 " --> pdb=" O LEU K 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 394 removed outlier: 6.241A pdb=" N GLU A 390 " --> pdb=" O ILE C 391 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LYS C 393 " --> pdb=" O GLU A 390 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER A 392 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU C 390 " --> pdb=" O ILE E 391 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LYS E 393 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER C 392 " --> pdb=" O LYS E 393 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 372 through 378 removed outlier: 6.732A pdb=" N SER F 373 " --> pdb=" O SER H 374 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N LYS H 376 " --> pdb=" O SER F 373 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE F 375 " --> pdb=" O LYS H 376 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N SER H 378 " --> pdb=" O ILE F 375 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU F 377 " --> pdb=" O SER H 378 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER H 373 " --> pdb=" O SER J 374 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N LYS J 376 " --> pdb=" O SER H 373 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE H 375 " --> pdb=" O LYS J 376 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N SER J 378 " --> pdb=" O ILE H 375 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU H 377 " --> pdb=" O SER J 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.548A pdb=" N ILE B 389 " --> pdb=" O GLU D 390 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N SER D 392 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE B 391 " --> pdb=" O SER D 392 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N SER D 394 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS B 393 " --> pdb=" O SER D 394 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE J 389 " --> pdb=" O GLU L 390 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N SER L 392 " --> pdb=" O ILE J 389 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE J 391 " --> pdb=" O SER L 392 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N SER L 394 " --> pdb=" O ILE J 391 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS J 393 " --> pdb=" O SER L 394 " (cutoff:3.500A) 51 hydrogen bonds defined for protein. 153 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: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 456 1.29 - 1.35: 396 1.35 - 1.42: 143 1.42 - 1.48: 349 1.48 - 1.54: 1032 Bond restraints: 2376 Sorted by residual: bond pdb=" N SER B 371 " pdb=" CA SER B 371 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N SER L 371 " pdb=" CA SER L 371 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 bond pdb=" N SER D 371 " pdb=" CA SER D 371 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.72e+00 bond pdb=" N SER F 371 " pdb=" CA SER F 371 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.66e+00 bond pdb=" N SER A 371 " pdb=" CA SER A 371 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.65e+00 ... (remaining 2371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.48: 2489 0.48 - 0.96: 489 0.96 - 1.44: 134 1.44 - 1.92: 58 1.92 - 2.40: 10 Bond angle restraints: 3180 Sorted by residual: angle pdb=" N ASN J 385 " pdb=" CA ASN J 385 " pdb=" CB ASN J 385 " ideal model delta sigma weight residual 112.30 110.23 2.07 1.52e+00 4.33e-01 1.86e+00 angle pdb=" N SER I 378 " pdb=" CA SER I 378 " pdb=" C SER I 378 " ideal model delta sigma weight residual 108.26 110.51 -2.25 1.66e+00 3.63e-01 1.84e+00 angle pdb=" N SER L 378 " pdb=" CA SER L 378 " pdb=" C SER L 378 " ideal model delta sigma weight residual 108.48 110.84 -2.36 1.80e+00 3.09e-01 1.72e+00 angle pdb=" N ASN H 381 " pdb=" CA ASN H 381 " pdb=" C ASN H 381 " ideal model delta sigma weight residual 109.50 111.47 -1.97 1.58e+00 4.01e-01 1.56e+00 angle pdb=" N SER C 378 " pdb=" CA SER C 378 " pdb=" C SER C 378 " ideal model delta sigma weight residual 108.48 110.70 -2.22 1.80e+00 3.09e-01 1.53e+00 ... (remaining 3175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 1448 16.34 - 32.68: 68 32.68 - 49.01: 4 49.01 - 65.35: 1 65.35 - 81.69: 3 Dihedral angle restraints: 1524 sinusoidal: 588 harmonic: 936 Sorted by residual: dihedral pdb=" CB GLU E 390 " pdb=" CG GLU E 390 " pdb=" CD GLU E 390 " pdb=" OE1 GLU E 390 " ideal model delta sinusoidal sigma weight residual 0.00 -81.69 81.69 1 3.00e+01 1.11e-03 9.12e+00 dihedral pdb=" CA SER C 371 " pdb=" C SER C 371 " pdb=" N TYR C 372 " pdb=" CA TYR C 372 " ideal model delta harmonic sigma weight residual 180.00 165.68 14.32 0 5.00e+00 4.00e-02 8.21e+00 dihedral pdb=" CA GLU B 390 " pdb=" CB GLU B 390 " pdb=" CG GLU B 390 " pdb=" CD GLU B 390 " ideal model delta sinusoidal sigma weight residual -60.00 -104.84 44.84 3 1.50e+01 4.44e-03 8.07e+00 ... (remaining 1521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 161 0.026 - 0.052: 125 0.052 - 0.078: 38 0.078 - 0.103: 4 0.103 - 0.129: 32 Chirality restraints: 360 Sorted by residual: chirality pdb=" CA ILE C 389 " pdb=" N ILE C 389 " pdb=" C ILE C 389 " pdb=" CB ILE C 389 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE F 375 " pdb=" N ILE F 375 " pdb=" C ILE F 375 " pdb=" CB ILE F 375 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA ILE D 375 " pdb=" N ILE D 375 " pdb=" C ILE D 375 " pdb=" CB ILE D 375 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 357 not shown) Planarity restraints: 432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 385 " 0.005 2.00e-02 2.50e+03 9.48e-03 8.99e-01 pdb=" CG ASN F 385 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN F 385 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN F 385 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 385 " 0.004 2.00e-02 2.50e+03 8.70e-03 7.58e-01 pdb=" CG ASN D 385 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN D 385 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN D 385 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN H 385 " 0.002 2.00e-02 2.50e+03 4.96e-03 2.46e-01 pdb=" CG ASN H 385 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN H 385 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN H 385 " 0.003 2.00e-02 2.50e+03 ... (remaining 429 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 12 2.67 - 3.23: 2391 3.23 - 3.78: 3963 3.78 - 4.34: 5703 4.34 - 4.90: 9361 Nonbonded interactions: 21430 Sorted by model distance: nonbonded pdb=" NZ LYS A 393 " pdb=" OG SER E 371 " model vdw 2.112 3.120 nonbonded pdb=" OG SER F 378 " pdb=" OD1 ASN F 379 " model vdw 2.319 3.040 nonbonded pdb=" OG SER B 378 " pdb=" OD1 ASN B 379 " model vdw 2.390 3.040 nonbonded pdb=" OG SER D 378 " pdb=" OD1 ASN D 379 " model vdw 2.400 3.040 nonbonded pdb=" OE2 GLU J 390 " pdb=" NZ LYS K 376 " model vdw 2.482 3.120 ... (remaining 21425 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.020 Find NCS groups from input model: 0.110 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:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 0.033 2376 Z= 0.234 Angle : 0.475 2.401 3180 Z= 0.291 Chirality : 0.048 0.129 360 Planarity : 0.001 0.009 432 Dihedral : 10.271 81.689 900 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.19 (0.56), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.15 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR G 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.302 Fit side-chains REVERT: I 392 SER cc_start: 0.8773 (m) cc_final: 0.8453 (m) REVERT: L 390 GLU cc_start: 0.8275 (tt0) cc_final: 0.8061 (tt0) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.7982 time to fit residues: 85.5324 Evaluate side-chains 86 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.0470 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 ASN B 383 ASN F 379 ASN ** F 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 387 ASN L 387 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2376 Z= 0.264 Angle : 0.527 4.509 3180 Z= 0.312 Chirality : 0.050 0.144 360 Planarity : 0.002 0.008 432 Dihedral : 5.713 17.163 312 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.53 % Allowed : 14.74 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.56), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.24 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR J 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.282 Fit side-chains REVERT: G 392 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8763 (p) REVERT: J 375 ILE cc_start: 0.9146 (mt) cc_final: 0.8798 (mp) outliers start: 11 outliers final: 8 residues processed: 95 average time/residue: 0.8596 time to fit residues: 84.1081 Evaluate side-chains 95 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 385 ASN Chi-restraints excluded: chain I residue 377 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 17 optimal weight: 0.3980 chunk 16 optimal weight: 0.0970 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2376 Z= 0.191 Angle : 0.493 4.287 3180 Z= 0.291 Chirality : 0.049 0.135 360 Planarity : 0.002 0.006 432 Dihedral : 5.502 14.711 312 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.17 % Allowed : 15.38 % Favored : 80.45 % 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: 0.45 (0.57), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.36 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR J 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.284 Fit side-chains REVERT: C 379 ASN cc_start: 0.8765 (m110) cc_final: 0.8546 (m110) REVERT: G 392 SER cc_start: 0.9020 (OUTLIER) cc_final: 0.8742 (p) REVERT: J 375 ILE cc_start: 0.9150 (mt) cc_final: 0.8789 (mp) outliers start: 13 outliers final: 10 residues processed: 92 average time/residue: 0.7886 time to fit residues: 74.8199 Evaluate side-chains 99 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 385 ASN Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 392 SER Chi-restraints excluded: chain L residue 378 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 379 ASN ** F 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2376 Z= 0.312 Angle : 0.567 4.663 3180 Z= 0.328 Chirality : 0.050 0.135 360 Planarity : 0.002 0.013 432 Dihedral : 5.804 17.793 312 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.49 % Allowed : 16.99 % Favored : 78.53 % 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: 0.30 (0.56), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.24 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR J 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: G 392 SER cc_start: 0.9047 (OUTLIER) cc_final: 0.8762 (p) outliers start: 14 outliers final: 12 residues processed: 90 average time/residue: 0.9218 time to fit residues: 85.2847 Evaluate side-chains 97 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 385 ASN Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 392 SER Chi-restraints excluded: chain K residue 376 LYS Chi-restraints excluded: chain L residue 378 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.0770 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.0270 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 379 ASN ** F 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2376 Z= 0.181 Angle : 0.512 4.678 3180 Z= 0.297 Chirality : 0.049 0.129 360 Planarity : 0.001 0.012 432 Dihedral : 5.534 14.129 312 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.49 % Allowed : 17.31 % Favored : 78.21 % 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: 0.39 (0.56), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.31 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR J 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: G 392 SER cc_start: 0.9002 (OUTLIER) cc_final: 0.8731 (p) REVERT: H 393 LYS cc_start: 0.8334 (mttp) cc_final: 0.8113 (mptm) REVERT: J 375 ILE cc_start: 0.9121 (mt) cc_final: 0.8761 (mp) outliers start: 14 outliers final: 12 residues processed: 90 average time/residue: 0.8840 time to fit residues: 81.8647 Evaluate side-chains 100 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 385 ASN Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 392 SER Chi-restraints excluded: chain K residue 376 LYS Chi-restraints excluded: chain L residue 378 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 379 ASN ** F 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2376 Z= 0.346 Angle : 0.590 4.525 3180 Z= 0.337 Chirality : 0.050 0.132 360 Planarity : 0.002 0.013 432 Dihedral : 5.814 17.511 312 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.13 % Allowed : 17.31 % Favored : 77.56 % 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: 0.23 (0.55), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.19 (0.42), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR J 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: G 392 SER cc_start: 0.9043 (OUTLIER) cc_final: 0.8754 (p) REVERT: H 393 LYS cc_start: 0.8339 (mttp) cc_final: 0.8128 (mptm) outliers start: 16 outliers final: 13 residues processed: 87 average time/residue: 0.8890 time to fit residues: 79.5612 Evaluate side-chains 94 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 385 ASN Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 392 SER Chi-restraints excluded: chain L residue 378 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.0770 chunk 11 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.0770 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 379 ASN ** F 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2376 Z= 0.156 Angle : 0.531 6.092 3180 Z= 0.297 Chirality : 0.049 0.129 360 Planarity : 0.001 0.012 432 Dihedral : 5.435 13.237 312 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.17 % Allowed : 18.59 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.56), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.39 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR J 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: L 394 SER cc_start: 0.8286 (t) cc_final: 0.7733 (p) outliers start: 13 outliers final: 12 residues processed: 90 average time/residue: 0.8461 time to fit residues: 78.3820 Evaluate side-chains 97 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 385 ASN Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 392 SER Chi-restraints excluded: chain K residue 378 SER Chi-restraints excluded: chain L residue 378 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.0370 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 379 ASN ** F 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2376 Z= 0.228 Angle : 0.564 6.707 3180 Z= 0.315 Chirality : 0.049 0.129 360 Planarity : 0.002 0.013 432 Dihedral : 5.618 14.835 312 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.13 % Allowed : 18.91 % Favored : 75.96 % 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: 0.51 (0.56), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.40 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR J 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: F 393 LYS cc_start: 0.8325 (mtmt) cc_final: 0.8049 (mttp) outliers start: 16 outliers final: 13 residues processed: 89 average time/residue: 0.8710 time to fit residues: 79.7530 Evaluate side-chains 100 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 385 ASN Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 392 SER Chi-restraints excluded: chain K residue 378 SER Chi-restraints excluded: chain L residue 378 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.0040 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.0570 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.3910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 379 ASN ** F 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2376 Z= 0.208 Angle : 0.569 6.871 3180 Z= 0.315 Chirality : 0.049 0.134 360 Planarity : 0.001 0.013 432 Dihedral : 5.607 14.562 312 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.81 % Allowed : 19.55 % Favored : 75.64 % 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: 0.57 (0.56), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.44 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR J 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.316 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 89 average time/residue: 0.8544 time to fit residues: 78.2956 Evaluate side-chains 100 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 385 ASN Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 392 SER Chi-restraints excluded: chain L residue 378 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 379 ASN ** F 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2376 Z= 0.262 Angle : 0.588 7.155 3180 Z= 0.328 Chirality : 0.050 0.136 360 Planarity : 0.002 0.013 432 Dihedral : 5.767 15.783 312 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.85 % Allowed : 21.15 % Favored : 75.00 % 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: 0.53 (0.56), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.41 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR J 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.311 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 12 residues processed: 89 average time/residue: 0.8516 time to fit residues: 78.0880 Evaluate side-chains 97 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain G residue 374 SER Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 385 ASN Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 392 SER Chi-restraints excluded: chain L residue 378 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 23 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 0.0870 chunk 22 optimal weight: 0.0060 chunk 10 optimal weight: 1.9990 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 379 ASN ** F 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.124176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.098614 restraints weight = 2553.769| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.96 r_work: 0.3460 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2376 Z= 0.168 Angle : 0.553 6.807 3180 Z= 0.306 Chirality : 0.049 0.134 360 Planarity : 0.001 0.013 432 Dihedral : 5.489 13.237 312 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.17 % Allowed : 20.83 % Favored : 75.00 % 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: 0.66 (0.57), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.51 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR J 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1955.76 seconds wall clock time: 35 minutes 20.64 seconds (2120.64 seconds total)