Starting phenix.real_space_refine on Wed Sep 17 03:00:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c1u_45130/09_2025/9c1u_45130.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c1u_45130/09_2025/9c1u_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 { model { file = "/net/cci-nas-00/data/ceres_data/9c1u_45130/09_2025/9c1u_45130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c1u_45130/09_2025/9c1u_45130.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c1u_45130/09_2025/9c1u_45130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c1u_45130/09_2025/9c1u_45130.map" } resolution = 2.31 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 0.69, per 1000 atoms: 0.29 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: 0.17 Conformation dependent library (CDL) restraints added in 95.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.09 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: 0.32 Time building geometry restraints manager: 0.25 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: 2.080 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.360 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.830 ------------------------------------------------------------------------------- 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= 0.186 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 2376) covalent geometry : angle 0.47473 ( 3180) hydrogen bonds : bond 0.11259 ( 51) hydrogen bonds : angle 6.82398 ( 153) *********************** 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 : 0.107 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: 0.3893 time to fit residues: 41.6400 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 : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 11 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.120811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.095658 restraints weight = 2573.948| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.98 r_work: 0.3408 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2376 Z= 0.167 Angle : 0.520 4.502 3180 Z= 0.307 Chirality : 0.050 0.142 360 Planarity : 0.002 0.008 432 Dihedral : 5.670 16.610 312 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.53 % Allowed : 14.10 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.56), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.26 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR J 372 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 2376) covalent geometry : angle 0.51983 ( 3180) hydrogen bonds : bond 0.02954 ( 51) hydrogen bonds : angle 4.57978 ( 153) *********************** 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 : 0.076 Fit side-chains REVERT: G 392 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8771 (p) REVERT: J 375 ILE cc_start: 0.9035 (mt) cc_final: 0.8638 (mp) REVERT: L 378 SER cc_start: 0.8588 (t) cc_final: 0.8348 (m) REVERT: L 390 GLU cc_start: 0.8626 (tt0) cc_final: 0.8343 (tt0) outliers start: 11 outliers final: 8 residues processed: 95 average time/residue: 0.4107 time to fit residues: 40.1296 Evaluate side-chains 96 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.106 ------------------------------------------------------------------------------- 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 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.120514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.094625 restraints weight = 2646.428| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.01 r_work: 0.3387 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2376 Z= 0.184 Angle : 0.527 4.478 3180 Z= 0.310 Chirality : 0.049 0.139 360 Planarity : 0.002 0.006 432 Dihedral : 5.730 17.342 312 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.53 % Allowed : 15.71 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.56), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.23 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR J 372 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 2376) covalent geometry : angle 0.52749 ( 3180) hydrogen bonds : bond 0.02833 ( 51) hydrogen bonds : angle 4.06466 ( 153) *********************** 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 98 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.157 Fit side-chains REVERT: F 379 ASN cc_start: 0.9034 (m-40) cc_final: 0.8741 (m-40) REVERT: G 392 SER cc_start: 0.9056 (OUTLIER) cc_final: 0.8762 (p) REVERT: H 393 LYS cc_start: 0.8158 (mttm) cc_final: 0.7948 (mttp) REVERT: L 378 SER cc_start: 0.8648 (t) cc_final: 0.8402 (m) REVERT: L 385 ASN cc_start: 0.9188 (m110) cc_final: 0.8947 (m-40) REVERT: L 390 GLU cc_start: 0.8621 (tt0) cc_final: 0.8340 (tt0) outliers start: 11 outliers final: 10 residues processed: 91 average time/residue: 0.4187 time to fit residues: 39.1910 Evaluate side-chains 95 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 15 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.0570 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.121503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.095635 restraints weight = 2574.555| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.00 r_work: 0.3403 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2376 Z= 0.145 Angle : 0.506 4.430 3180 Z= 0.296 Chirality : 0.049 0.133 360 Planarity : 0.002 0.007 432 Dihedral : 5.582 15.129 312 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.17 % Allowed : 15.71 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.56), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.30 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR J 372 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 2376) covalent geometry : angle 0.50636 ( 3180) hydrogen bonds : bond 0.02310 ( 51) hydrogen bonds : angle 3.75207 ( 153) *********************** 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 101 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.113 Fit side-chains REVERT: F 379 ASN cc_start: 0.9046 (m-40) cc_final: 0.8731 (m-40) REVERT: G 392 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8734 (p) REVERT: H 393 LYS cc_start: 0.8168 (mttm) cc_final: 0.7940 (mttp) REVERT: J 375 ILE cc_start: 0.9002 (mt) cc_final: 0.8615 (mp) REVERT: L 378 SER cc_start: 0.8618 (t) cc_final: 0.8389 (m) REVERT: L 385 ASN cc_start: 0.9145 (m110) cc_final: 0.8894 (m-40) REVERT: L 390 GLU cc_start: 0.8601 (tt0) cc_final: 0.8328 (tt0) outliers start: 13 outliers final: 10 residues processed: 91 average time/residue: 0.3856 time to fit residues: 36.0790 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 : 0.100 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.120121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.094283 restraints weight = 2593.667| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.99 r_work: 0.3388 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2376 Z= 0.187 Angle : 0.555 5.006 3180 Z= 0.319 Chirality : 0.049 0.130 360 Planarity : 0.002 0.005 432 Dihedral : 5.776 16.924 312 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.53 % Allowed : 16.67 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (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 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 2376) covalent geometry : angle 0.55510 ( 3180) hydrogen bonds : bond 0.02530 ( 51) hydrogen bonds : angle 3.77769 ( 153) *********************** 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 98 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.096 Fit side-chains REVERT: F 379 ASN cc_start: 0.9068 (m-40) cc_final: 0.8747 (m-40) REVERT: G 392 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8742 (p) REVERT: H 393 LYS cc_start: 0.8180 (mttm) cc_final: 0.7972 (mttp) REVERT: L 378 SER cc_start: 0.8637 (t) cc_final: 0.8403 (m) REVERT: L 390 GLU cc_start: 0.8590 (tt0) cc_final: 0.8314 (tt0) outliers start: 11 outliers final: 10 residues processed: 90 average time/residue: 0.3923 time to fit residues: 36.3353 Evaluate side-chains 94 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.106 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.120241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.094493 restraints weight = 2590.816| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.98 r_work: 0.3391 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1961 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= 0.199 Angle : 0.554 5.144 3180 Z= 0.319 Chirality : 0.049 0.131 360 Planarity : 0.002 0.008 432 Dihedral : 5.762 16.653 312 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 3.85 % Allowed : 16.99 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.55), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.22 (0.42), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR J 372 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 2376) covalent geometry : angle 0.55377 ( 3180) hydrogen bonds : bond 0.02560 ( 51) hydrogen bonds : angle 3.79613 ( 153) *********************** 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 96 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.104 Fit side-chains REVERT: F 379 ASN cc_start: 0.9084 (m-40) cc_final: 0.8792 (m110) REVERT: G 392 SER cc_start: 0.9046 (OUTLIER) cc_final: 0.8767 (p) REVERT: H 393 LYS cc_start: 0.8172 (mttm) cc_final: 0.7956 (mttp) REVERT: L 378 SER cc_start: 0.8674 (t) cc_final: 0.8444 (m) REVERT: L 390 GLU cc_start: 0.8596 (tt0) cc_final: 0.8303 (tt0) outliers start: 12 outliers final: 11 residues processed: 87 average time/residue: 0.3675 time to fit residues: 32.8540 Evaluate side-chains 94 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.105 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 4 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.120329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.094658 restraints weight = 2610.288| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.97 r_work: 0.3391 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2376 Z= 0.202 Angle : 0.591 10.368 3180 Z= 0.327 Chirality : 0.050 0.129 360 Planarity : 0.002 0.005 432 Dihedral : 5.805 16.801 312 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.49 % Allowed : 17.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.55), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.18 (0.42), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR J 372 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 2376) covalent geometry : angle 0.59133 ( 3180) hydrogen bonds : bond 0.02506 ( 51) hydrogen bonds : angle 3.86756 ( 153) *********************** 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 97 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.106 Fit side-chains REVERT: C 390 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: E 394 SER cc_start: 0.8232 (m) cc_final: 0.7910 (p) REVERT: F 379 ASN cc_start: 0.9100 (m-40) cc_final: 0.8817 (m110) REVERT: G 392 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8749 (p) REVERT: H 393 LYS cc_start: 0.8178 (mttm) cc_final: 0.7963 (mttp) REVERT: L 378 SER cc_start: 0.8647 (t) cc_final: 0.8427 (m) REVERT: L 390 GLU cc_start: 0.8605 (tt0) cc_final: 0.8316 (tt0) outliers start: 14 outliers final: 11 residues processed: 87 average time/residue: 0.3271 time to fit residues: 29.3081 Evaluate side-chains 94 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 390 GLU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** ** L 385 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 = 0.3849 r_free = 0.3849 target = 0.120101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.094501 restraints weight = 2583.455| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.97 r_work: 0.3398 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2376 Z= 0.183 Angle : 0.568 6.806 3180 Z= 0.320 Chirality : 0.049 0.130 360 Planarity : 0.002 0.006 432 Dihedral : 5.784 16.086 312 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.87 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.55), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.18 (0.42), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR J 372 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 2376) covalent geometry : angle 0.56751 ( 3180) hydrogen bonds : bond 0.02404 ( 51) hydrogen bonds : angle 3.84602 ( 153) *********************** 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 98 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.061 Fit side-chains REVERT: C 390 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: E 394 SER cc_start: 0.8360 (m) cc_final: 0.8044 (p) REVERT: F 379 ASN cc_start: 0.9109 (m-40) cc_final: 0.8824 (m110) REVERT: G 392 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8740 (p) REVERT: H 393 LYS cc_start: 0.8183 (mttm) cc_final: 0.7970 (mttp) REVERT: L 378 SER cc_start: 0.8645 (t) cc_final: 0.8430 (m) REVERT: L 390 GLU cc_start: 0.8608 (tt0) cc_final: 0.8317 (tt0) outliers start: 14 outliers final: 12 residues processed: 88 average time/residue: 0.3147 time to fit residues: 28.4574 Evaluate side-chains 95 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 390 GLU 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 K residue 378 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** L 385 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 = 0.3851 r_free = 0.3851 target = 0.120465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.094526 restraints weight = 2605.128| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.97 r_work: 0.3392 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 2376 Z= 0.236 Angle : 0.645 10.304 3180 Z= 0.349 Chirality : 0.050 0.131 360 Planarity : 0.002 0.006 432 Dihedral : 5.962 17.398 312 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 4.17 % Allowed : 17.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.54), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.07 (0.41), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR J 372 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 2376) covalent geometry : angle 0.64506 ( 3180) hydrogen bonds : bond 0.02644 ( 51) hydrogen bonds : angle 4.06409 ( 153) *********************** 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 94 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.060 Fit side-chains REVERT: C 390 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7722 (mt-10) REVERT: E 394 SER cc_start: 0.8277 (m) cc_final: 0.7953 (p) REVERT: F 379 ASN cc_start: 0.9110 (m-40) cc_final: 0.8813 (m110) REVERT: G 392 SER cc_start: 0.9050 (OUTLIER) cc_final: 0.8760 (p) REVERT: H 393 LYS cc_start: 0.8180 (mttm) cc_final: 0.7939 (mttp) REVERT: L 378 SER cc_start: 0.8671 (t) cc_final: 0.8460 (m) REVERT: L 390 GLU cc_start: 0.8616 (tt0) cc_final: 0.8315 (tt0) outliers start: 13 outliers final: 10 residues processed: 85 average time/residue: 0.3409 time to fit residues: 29.7746 Evaluate side-chains 92 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 390 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** ** L 385 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 = 0.3866 r_free = 0.3866 target = 0.121549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.095698 restraints weight = 2599.018| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.98 r_work: 0.3405 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2120 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= 0.206 Angle : 0.600 7.171 3180 Z= 0.330 Chirality : 0.049 0.130 360 Planarity : 0.002 0.011 432 Dihedral : 5.832 15.872 312 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 4.81 % Allowed : 16.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.54), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.08 (0.41), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR J 372 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 2376) covalent geometry : angle 0.59968 ( 3180) hydrogen bonds : bond 0.02442 ( 51) hydrogen bonds : angle 3.98487 ( 153) ********************** 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 100 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.107 Fit side-chains REVERT: C 390 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: E 394 SER cc_start: 0.7984 (m) cc_final: 0.7661 (p) REVERT: F 379 ASN cc_start: 0.9114 (m-40) cc_final: 0.8810 (m110) REVERT: G 392 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8770 (p) REVERT: H 393 LYS cc_start: 0.8225 (mttm) cc_final: 0.7999 (mttp) REVERT: L 378 SER cc_start: 0.8661 (t) cc_final: 0.8459 (m) REVERT: L 390 GLU cc_start: 0.8621 (tt0) cc_final: 0.8323 (tt0) outliers start: 15 outliers final: 13 residues processed: 88 average time/residue: 0.3603 time to fit residues: 32.6391 Evaluate side-chains 100 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 390 GLU 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 K residue 376 LYS Chi-restraints excluded: chain K residue 378 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 20 optimal weight: 0.0870 chunk 10 optimal weight: 0.2980 overall best weight: 0.2558 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.124637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.099062 restraints weight = 2596.702| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.97 r_work: 0.3455 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2376 Z= 0.105 Angle : 0.525 6.811 3180 Z= 0.292 Chirality : 0.048 0.134 360 Planarity : 0.001 0.005 432 Dihedral : 5.426 12.440 312 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.53 % Allowed : 17.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.56), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.27 (0.43), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR J 372 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 2376) covalent geometry : angle 0.52462 ( 3180) hydrogen bonds : bond 0.01845 ( 51) hydrogen bonds : angle 3.58084 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1309.20 seconds wall clock time: 23 minutes 4.48 seconds (1384.48 seconds total)