Starting phenix.real_space_refine on Wed Mar 5 23:20:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bgs_16035/03_2025/8bgs_16035.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bgs_16035/03_2025/8bgs_16035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bgs_16035/03_2025/8bgs_16035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bgs_16035/03_2025/8bgs_16035.map" model { file = "/net/cci-nas-00/data/ceres_data/8bgs_16035/03_2025/8bgs_16035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bgs_16035/03_2025/8bgs_16035.cif" } resolution = 3.16 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 7 5.16 5 C 2520 2.51 5 N 742 2.21 5 O 749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4018 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Restraints were copied for chains: C, B, E, D, F, r Time building chain proxies: 2.26, per 1000 atoms: 0.56 Number of scatterers: 4018 At special positions: 0 Unit cell: (150.15, 72.45, 39.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 7 16.00 O 749 8.00 N 742 7.00 C 2520 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: 0.94 Conformation dependent library (CDL) restraints added in 1.1 seconds 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 924 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.632A pdb=" N GLN r 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR E 310 " --> pdb=" O GLN r 307 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL r 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN E 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR F 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL E 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.705A pdb=" N VAL r 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 318 removed outlier: 6.275A pdb=" N LYS r 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS E 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.372A pdb=" N ILE r 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.443A pdb=" N GLN r 336 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL E 339 " --> pdb=" O GLN r 336 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU r 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN E 336 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL F 339 " --> pdb=" O GLN E 336 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU E 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 351 through 353 removed outlier: 6.490A pdb=" N GLN r 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN E 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.537A pdb=" N ASN r 359 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N HIS B 362 " --> pdb=" O ASN r 359 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR r 361 " --> pdb=" O HIS B 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 376 through 377 removed outlier: 6.501A pdb=" N LEU r 376 " --> pdb=" O THR B 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.633A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLN C 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR D 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL C 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.705A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 317 through 318 removed outlier: 6.275A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LYS C 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AB4, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.442A pdb=" N GLN A 336 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL C 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU A 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN C 336 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL D 339 " --> pdb=" O GLN C 336 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU C 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 351 through 353 removed outlier: 6.490A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLN C 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 359 through 362 Processing sheet with id=AB7, first strand: chain 'A' and resid 376 through 377 36 hydrogen bonds defined for protein. 108 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: 0.92 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 945 1.33 - 1.45: 912 1.45 - 1.57: 2217 1.57 - 1.70: 0 1.70 - 1.82: 7 Bond restraints: 4081 Sorted by residual: bond pdb=" CB HIS C 362 " pdb=" CG HIS C 362 " ideal model delta sigma weight residual 1.497 1.458 0.039 1.40e-02 5.10e+03 7.93e+00 bond pdb=" CB HIS E 362 " pdb=" CG HIS E 362 " ideal model delta sigma weight residual 1.497 1.458 0.039 1.40e-02 5.10e+03 7.93e+00 bond pdb=" CB HIS F 362 " pdb=" CG HIS F 362 " ideal model delta sigma weight residual 1.497 1.458 0.039 1.40e-02 5.10e+03 7.90e+00 bond pdb=" CB HIS D 362 " pdb=" CG HIS D 362 " ideal model delta sigma weight residual 1.497 1.458 0.039 1.40e-02 5.10e+03 7.84e+00 bond pdb=" CB HIS A 362 " pdb=" CG HIS A 362 " ideal model delta sigma weight residual 1.497 1.458 0.039 1.40e-02 5.10e+03 7.80e+00 ... (remaining 4076 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 4256 1.95 - 3.89: 1099 3.89 - 5.84: 91 5.84 - 7.79: 7 7.79 - 9.74: 7 Bond angle restraints: 5460 Sorted by residual: angle pdb=" N PRO A 332 " pdb=" CA PRO A 332 " pdb=" C PRO A 332 " ideal model delta sigma weight residual 110.21 119.95 -9.74 1.64e+00 3.72e-01 3.52e+01 angle pdb=" N PRO B 332 " pdb=" CA PRO B 332 " pdb=" C PRO B 332 " ideal model delta sigma weight residual 110.21 119.94 -9.73 1.64e+00 3.72e-01 3.52e+01 angle pdb=" N PRO C 332 " pdb=" CA PRO C 332 " pdb=" C PRO C 332 " ideal model delta sigma weight residual 110.21 119.93 -9.72 1.64e+00 3.72e-01 3.51e+01 angle pdb=" N PRO E 332 " pdb=" CA PRO E 332 " pdb=" C PRO E 332 " ideal model delta sigma weight residual 110.21 119.93 -9.72 1.64e+00 3.72e-01 3.51e+01 angle pdb=" N PRO D 332 " pdb=" CA PRO D 332 " pdb=" C PRO D 332 " ideal model delta sigma weight residual 110.21 119.93 -9.72 1.64e+00 3.72e-01 3.51e+01 ... (remaining 5455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.14: 2170 13.14 - 26.28: 231 26.28 - 39.41: 56 39.41 - 52.55: 28 52.55 - 65.69: 7 Dihedral angle restraints: 2492 sinusoidal: 1043 harmonic: 1449 Sorted by residual: dihedral pdb=" CA LYS B 321 " pdb=" C LYS B 321 " pdb=" N CYS B 322 " pdb=" CA CYS B 322 " ideal model delta harmonic sigma weight residual -180.00 -148.63 -31.37 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA LYS D 321 " pdb=" C LYS D 321 " pdb=" N CYS D 322 " pdb=" CA CYS D 322 " ideal model delta harmonic sigma weight residual -180.00 -148.64 -31.36 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CA LYS C 321 " pdb=" C LYS C 321 " pdb=" N CYS C 322 " pdb=" CA CYS C 322 " ideal model delta harmonic sigma weight residual 180.00 -148.65 -31.35 0 5.00e+00 4.00e-02 3.93e+01 ... (remaining 2489 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.059: 259 0.059 - 0.116: 224 0.116 - 0.172: 84 0.172 - 0.229: 42 0.229 - 0.286: 7 Chirality restraints: 616 Sorted by residual: chirality pdb=" CA LYS E 347 " pdb=" N LYS E 347 " pdb=" C LYS E 347 " pdb=" CB LYS E 347 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA LYS C 347 " pdb=" N LYS C 347 " pdb=" C LYS C 347 " pdb=" CB LYS C 347 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA LYS r 347 " pdb=" N LYS r 347 " pdb=" C LYS r 347 " pdb=" CB LYS r 347 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 613 not shown) Planarity restraints: 693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 334 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C GLY B 334 " 0.033 2.00e-02 2.50e+03 pdb=" O GLY B 334 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY B 335 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 334 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C GLY E 334 " 0.033 2.00e-02 2.50e+03 pdb=" O GLY E 334 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY E 335 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 334 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C GLY F 334 " 0.033 2.00e-02 2.50e+03 pdb=" O GLY F 334 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY F 335 " -0.011 2.00e-02 2.50e+03 ... (remaining 690 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 1370 2.87 - 3.38: 3423 3.38 - 3.89: 6494 3.89 - 4.39: 7137 4.39 - 4.90: 14326 Nonbonded interactions: 32750 Sorted by model distance: nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.368 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.368 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.369 3.040 nonbonded pdb=" OD1 ASP r 314 " pdb=" OG SER r 316 " model vdw 2.369 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.369 3.040 ... (remaining 32745 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' selection = chain 'r' } 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: 1.530 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.680 Find NCS groups from input model: 0.090 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 0.009 0.043 4081 Z= 0.628 Angle : 1.642 9.736 5460 Z= 1.123 Chirality : 0.095 0.286 616 Planarity : 0.009 0.043 693 Dihedral : 13.075 65.689 1568 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.41 % 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: -3.72 (0.26), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.20), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.004 HIS B 330 PHE 0.010 0.004 PHE D 378 TYR 0.025 0.009 TYR C 310 ARG 0.007 0.002 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 345 ASP cc_start: 0.8517 (t0) cc_final: 0.8316 (t0) REVERT: A 316 SER cc_start: 0.9053 (p) cc_final: 0.8612 (p) REVERT: C 353 LYS cc_start: 0.8959 (mtpt) cc_final: 0.8571 (mtpt) REVERT: F 316 SER cc_start: 0.8981 (p) cc_final: 0.8624 (p) REVERT: F 331 LYS cc_start: 0.9181 (mtpt) cc_final: 0.8058 (tmtt) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2585 time to fit residues: 31.2871 Evaluate side-chains 82 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: r 330 HIS r 362 HIS A 330 HIS ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS B 330 HIS B 362 HIS C 330 HIS C 362 HIS D 330 HIS D 336 GLN D 362 HIS E 330 HIS E 362 HIS F 330 HIS F 362 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.148868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.122520 restraints weight = 4315.154| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.61 r_work: 0.3827 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4081 Z= 0.269 Angle : 0.782 12.729 5460 Z= 0.388 Chirality : 0.053 0.141 616 Planarity : 0.003 0.029 693 Dihedral : 7.666 22.325 539 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 1.08 % Allowed : 13.64 % Favored : 85.28 % 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: -2.93 (0.28), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 330 PHE 0.005 0.001 PHE A 346 TYR 0.010 0.002 TYR r 310 ARG 0.004 0.001 ARG r 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.499 Fit side-chains REVERT: r 340 LYS cc_start: 0.8350 (mttt) cc_final: 0.7911 (mptt) REVERT: r 369 LYS cc_start: 0.8176 (mttt) cc_final: 0.7515 (mtpp) REVERT: A 311 LYS cc_start: 0.8248 (tttm) cc_final: 0.7726 (ttmt) REVERT: A 331 LYS cc_start: 0.8806 (mtpt) cc_final: 0.7370 (tptp) REVERT: A 340 LYS cc_start: 0.8479 (mttt) cc_final: 0.8037 (mptt) REVERT: A 369 LYS cc_start: 0.8131 (mttt) cc_final: 0.7873 (mttt) REVERT: B 311 LYS cc_start: 0.8449 (tttm) cc_final: 0.7895 (ttmt) REVERT: B 340 LYS cc_start: 0.8663 (mttt) cc_final: 0.8372 (mttm) REVERT: D 311 LYS cc_start: 0.8541 (tttm) cc_final: 0.8025 (ttmt) REVERT: D 315 LEU cc_start: 0.8796 (tt) cc_final: 0.8582 (mp) REVERT: D 372 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8454 (tp30) REVERT: E 311 LYS cc_start: 0.8248 (tttt) cc_final: 0.7729 (ttmt) REVERT: E 331 LYS cc_start: 0.9046 (mtpt) cc_final: 0.8691 (mtpp) REVERT: E 372 GLU cc_start: 0.8439 (tp30) cc_final: 0.8222 (tp30) REVERT: F 315 LEU cc_start: 0.8583 (tt) cc_final: 0.8317 (mp) REVERT: F 372 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8049 (mm-30) outliers start: 5 outliers final: 2 residues processed: 103 average time/residue: 0.2589 time to fit residues: 30.6546 Evaluate side-chains 85 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain F residue 353 LYS Chi-restraints excluded: chain F residue 372 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** 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 = 0.4207 r_free = 0.4207 target = 0.141377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.117677 restraints weight = 4553.889| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.41 r_work: 0.3786 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4081 Z= 0.358 Angle : 0.741 13.739 5460 Z= 0.379 Chirality : 0.053 0.142 616 Planarity : 0.004 0.032 693 Dihedral : 7.195 19.297 539 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.30 % Allowed : 17.32 % Favored : 81.39 % 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: -2.67 (0.30), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS r 362 PHE 0.004 0.001 PHE E 346 TYR 0.017 0.004 TYR r 310 ARG 0.004 0.000 ARG r 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8425 (mttt) cc_final: 0.8006 (mptt) REVERT: D 311 LYS cc_start: 0.8665 (tttm) cc_final: 0.8224 (ttmt) REVERT: D 372 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8231 (tp30) REVERT: E 331 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8655 (mtpp) REVERT: F 342 GLU cc_start: 0.4605 (pm20) cc_final: 0.3321 (mm-30) REVERT: F 372 GLU cc_start: 0.8348 (tp30) cc_final: 0.8040 (mm-30) outliers start: 6 outliers final: 5 residues processed: 85 average time/residue: 0.2298 time to fit residues: 22.9737 Evaluate side-chains 81 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 371 ILE Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 336 GLN ** 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 = 0.4221 r_free = 0.4221 target = 0.142100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.118819 restraints weight = 4615.623| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.40 r_work: 0.3803 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4081 Z= 0.295 Angle : 0.649 6.453 5460 Z= 0.339 Chirality : 0.051 0.137 616 Planarity : 0.004 0.034 693 Dihedral : 6.727 22.447 539 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.95 % Allowed : 16.88 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.66 (0.31), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS r 374 PHE 0.004 0.001 PHE E 346 TYR 0.014 0.003 TYR A 310 ARG 0.005 0.000 ARG r 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8167 (tttm) cc_final: 0.7643 (ttmt) REVERT: A 331 LYS cc_start: 0.8783 (mtpt) cc_final: 0.7367 (tptt) REVERT: A 340 LYS cc_start: 0.8459 (mttt) cc_final: 0.7967 (mmtm) REVERT: A 343 LYS cc_start: 0.7932 (ptmm) cc_final: 0.5715 (tppt) REVERT: A 369 LYS cc_start: 0.8170 (mttt) cc_final: 0.7828 (mttt) REVERT: B 336 GLN cc_start: 0.8913 (tt0) cc_final: 0.8671 (tt0) REVERT: C 342 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7218 (mm-30) REVERT: D 311 LYS cc_start: 0.8624 (tttm) cc_final: 0.8215 (ttmt) REVERT: D 372 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8266 (tp30) REVERT: E 331 LYS cc_start: 0.9055 (mtpt) cc_final: 0.8668 (mtpp) REVERT: F 372 GLU cc_start: 0.8269 (tp30) cc_final: 0.7868 (mm-30) outliers start: 9 outliers final: 6 residues processed: 86 average time/residue: 0.2441 time to fit residues: 24.5282 Evaluate side-chains 85 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 371 ILE Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 36 optimal weight: 0.2980 chunk 37 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** D 336 GLN ** 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 = 0.4276 r_free = 0.4276 target = 0.146485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.123003 restraints weight = 4641.457| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.44 r_work: 0.3860 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4081 Z= 0.215 Angle : 0.588 6.941 5460 Z= 0.305 Chirality : 0.050 0.125 616 Planarity : 0.003 0.031 693 Dihedral : 6.234 20.783 539 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 1.30 % Allowed : 17.32 % Favored : 81.39 % 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: -2.60 (0.31), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.004 0.001 PHE r 346 TYR 0.010 0.002 TYR r 310 ARG 0.002 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.8770 (mtpt) cc_final: 0.7360 (tptt) REVERT: A 343 LYS cc_start: 0.7902 (ptmm) cc_final: 0.5618 (tppt) REVERT: A 345 ASP cc_start: 0.7847 (t0) cc_final: 0.7591 (t0) REVERT: A 369 LYS cc_start: 0.8189 (mttt) cc_final: 0.7838 (mttt) REVERT: B 336 GLN cc_start: 0.8894 (tt0) cc_final: 0.8684 (tt0) REVERT: B 359 ASN cc_start: 0.8932 (m-40) cc_final: 0.8382 (m-40) REVERT: D 372 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8325 (tp30) REVERT: E 331 LYS cc_start: 0.9036 (mtpt) cc_final: 0.8654 (mtpp) REVERT: F 372 GLU cc_start: 0.8232 (tp30) cc_final: 0.7883 (mm-30) outliers start: 6 outliers final: 4 residues processed: 81 average time/residue: 0.2322 time to fit residues: 22.1500 Evaluate side-chains 81 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 371 ILE Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** 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 = 0.4188 r_free = 0.4188 target = 0.138840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.115871 restraints weight = 4680.874| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.38 r_work: 0.3770 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 4081 Z= 0.408 Angle : 0.685 7.731 5460 Z= 0.360 Chirality : 0.052 0.143 616 Planarity : 0.004 0.034 693 Dihedral : 6.661 19.762 539 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.60 % Allowed : 18.18 % Favored : 79.22 % 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: -2.78 (0.31), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 362 PHE 0.005 0.001 PHE r 346 TYR 0.017 0.004 TYR C 310 ARG 0.006 0.001 ARG r 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.8791 (mtpt) cc_final: 0.7308 (tptt) REVERT: A 343 LYS cc_start: 0.7936 (ptmm) cc_final: 0.5882 (tppt) REVERT: A 369 LYS cc_start: 0.8250 (mttt) cc_final: 0.7885 (mttt) REVERT: C 342 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7376 (mm-30) REVERT: D 372 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8328 (tp30) REVERT: E 331 LYS cc_start: 0.9043 (mtpt) cc_final: 0.8648 (mtpp) REVERT: F 372 GLU cc_start: 0.8237 (tp30) cc_final: 0.7877 (mm-30) outliers start: 12 outliers final: 8 residues processed: 90 average time/residue: 0.2274 time to fit residues: 24.1936 Evaluate side-chains 91 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 371 ILE Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** 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 = 0.4201 r_free = 0.4201 target = 0.139343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.116309 restraints weight = 4643.639| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.37 r_work: 0.3784 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4081 Z= 0.366 Angle : 0.676 7.987 5460 Z= 0.354 Chirality : 0.052 0.141 616 Planarity : 0.004 0.032 693 Dihedral : 6.548 19.161 539 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.16 % Allowed : 19.05 % Favored : 78.79 % 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: -2.82 (0.31), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 362 PHE 0.005 0.001 PHE A 378 TYR 0.015 0.004 TYR A 310 ARG 0.004 0.000 ARG r 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 SER cc_start: 0.8279 (m) cc_final: 0.8009 (t) REVERT: A 331 LYS cc_start: 0.8790 (mtpt) cc_final: 0.7258 (tptt) REVERT: A 343 LYS cc_start: 0.8148 (ptmm) cc_final: 0.6020 (tppt) REVERT: A 345 ASP cc_start: 0.7859 (t0) cc_final: 0.7597 (t0) REVERT: A 369 LYS cc_start: 0.8279 (mttt) cc_final: 0.7918 (mttt) REVERT: C 342 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7485 (mm-30) REVERT: D 372 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8283 (tp30) REVERT: E 331 LYS cc_start: 0.9045 (mtpt) cc_final: 0.8656 (mtpp) REVERT: F 372 GLU cc_start: 0.8229 (tp30) cc_final: 0.7883 (mm-30) outliers start: 10 outliers final: 10 residues processed: 91 average time/residue: 0.2311 time to fit residues: 24.7205 Evaluate side-chains 95 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 371 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN ** D 336 GLN ** 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 = 0.4254 r_free = 0.4254 target = 0.143908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.120362 restraints weight = 4500.951| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.40 r_work: 0.3845 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4081 Z= 0.247 Angle : 0.614 8.026 5460 Z= 0.318 Chirality : 0.050 0.127 616 Planarity : 0.004 0.032 693 Dihedral : 6.184 18.592 539 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.60 % Allowed : 19.26 % Favored : 78.14 % 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: -2.77 (0.31), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.004 0.001 PHE C 346 TYR 0.010 0.002 TYR C 310 ARG 0.005 0.000 ARG r 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 SER cc_start: 0.8119 (m) cc_final: 0.7910 (t) REVERT: A 331 LYS cc_start: 0.8788 (mtpt) cc_final: 0.7414 (tptt) REVERT: A 343 LYS cc_start: 0.8168 (ptmm) cc_final: 0.6060 (tppt) REVERT: A 345 ASP cc_start: 0.7834 (t0) cc_final: 0.7536 (t0) REVERT: A 369 LYS cc_start: 0.8274 (mttt) cc_final: 0.7952 (mttt) REVERT: B 340 LYS cc_start: 0.8692 (mttt) cc_final: 0.8422 (mttm) REVERT: B 359 ASN cc_start: 0.8949 (m-40) cc_final: 0.8409 (m-40) REVERT: C 342 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7491 (mm-30) REVERT: E 331 LYS cc_start: 0.9053 (mtpt) cc_final: 0.8676 (mtpp) REVERT: E 340 LYS cc_start: 0.8466 (mttt) cc_final: 0.8088 (mttm) REVERT: F 372 GLU cc_start: 0.8202 (tp30) cc_final: 0.7888 (mm-30) outliers start: 12 outliers final: 11 residues processed: 95 average time/residue: 0.2757 time to fit residues: 30.4962 Evaluate side-chains 102 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 371 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 34 optimal weight: 0.0040 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 336 GLN ** 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 = 0.4222 r_free = 0.4222 target = 0.140665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.117396 restraints weight = 4657.538| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.41 r_work: 0.3802 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4081 Z= 0.322 Angle : 0.657 8.448 5460 Z= 0.342 Chirality : 0.051 0.135 616 Planarity : 0.004 0.031 693 Dihedral : 6.307 18.477 539 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.60 % Allowed : 19.70 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.31), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.005 0.001 PHE r 346 TYR 0.014 0.003 TYR B 310 ARG 0.004 0.000 ARG r 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 SER cc_start: 0.8259 (m) cc_final: 0.7995 (t) REVERT: A 331 LYS cc_start: 0.8838 (mtpt) cc_final: 0.7394 (tptt) REVERT: A 343 LYS cc_start: 0.8174 (ptmm) cc_final: 0.6057 (tppt) REVERT: A 369 LYS cc_start: 0.8333 (mttt) cc_final: 0.7980 (mttt) REVERT: C 342 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7530 (mm-30) REVERT: D 372 GLU cc_start: 0.8563 (tp30) cc_final: 0.8296 (mt-10) REVERT: E 331 LYS cc_start: 0.9055 (mtpt) cc_final: 0.8679 (mtpp) REVERT: E 340 LYS cc_start: 0.8524 (mttt) cc_final: 0.8135 (mttm) REVERT: E 342 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8051 (mm-30) REVERT: F 372 GLU cc_start: 0.8247 (tp30) cc_final: 0.7902 (mm-30) outliers start: 12 outliers final: 11 residues processed: 92 average time/residue: 0.2479 time to fit residues: 26.5882 Evaluate side-chains 99 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 371 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 336 GLN ** 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 = 0.4220 r_free = 0.4220 target = 0.141090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.117597 restraints weight = 4610.258| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.37 r_work: 0.3804 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4081 Z= 0.317 Angle : 0.656 8.850 5460 Z= 0.340 Chirality : 0.051 0.136 616 Planarity : 0.004 0.034 693 Dihedral : 6.295 18.133 539 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.38 % Allowed : 19.48 % Favored : 78.14 % 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: -2.88 (0.31), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.004 0.001 PHE r 346 TYR 0.014 0.003 TYR A 310 ARG 0.004 0.000 ARG r 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1022 Ramachandran restraints generated. 511 Oldfield, 0 Emsley, 511 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 SER cc_start: 0.8226 (m) cc_final: 0.7990 (t) REVERT: A 331 LYS cc_start: 0.8834 (mtpt) cc_final: 0.7396 (tptt) REVERT: A 343 LYS cc_start: 0.8183 (ptmm) cc_final: 0.6069 (tppt) REVERT: A 369 LYS cc_start: 0.8343 (mttt) cc_final: 0.7994 (mttt) REVERT: B 311 LYS cc_start: 0.8461 (tttm) cc_final: 0.8029 (ttmt) REVERT: C 342 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7526 (mm-30) REVERT: D 372 GLU cc_start: 0.8541 (tp30) cc_final: 0.8186 (mt-10) REVERT: E 331 LYS cc_start: 0.9057 (mtpt) cc_final: 0.8685 (mtpp) REVERT: E 340 LYS cc_start: 0.8537 (mttt) cc_final: 0.8145 (mttm) REVERT: E 342 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7964 (mm-30) outliers start: 11 outliers final: 11 residues processed: 93 average time/residue: 0.2458 time to fit residues: 26.7775 Evaluate side-chains 99 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 371 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 33 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 0.4980 chunk 8 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.140553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.117237 restraints weight = 4630.877| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.40 r_work: 0.3799 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4081 Z= 0.331 Angle : 0.663 8.929 5460 Z= 0.345 Chirality : 0.051 0.138 616 Planarity : 0.004 0.035 693 Dihedral : 6.311 18.421 539 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.60 % Allowed : 19.26 % Favored : 78.14 % 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: -2.91 (0.31), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.005 0.001 PHE r 346 TYR 0.015 0.004 TYR r 310 ARG 0.004 0.000 ARG r 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2424.59 seconds wall clock time: 42 minutes 52.96 seconds (2572.96 seconds total)