Starting phenix.real_space_refine on Sun Mar 10 18:38:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgs_16035/03_2024/8bgs_16035.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgs_16035/03_2024/8bgs_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgs_16035/03_2024/8bgs_16035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgs_16035/03_2024/8bgs_16035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgs_16035/03_2024/8bgs_16035.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bgs_16035/03_2024/8bgs_16035.pdb" } 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 Residue "r ARG 349": "NH1" <-> "NH2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "F ARG 349": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4018 Number of models: 1 Model: "" Number of chains: 7 Chain: "r" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} 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} Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 3.45, per 1000 atoms: 0.86 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 937.6 milliseconds 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: 0.58 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: 0.89 Time building geometry restraints manager: 1.62 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: 101.27 - 108.04: 349 108.04 - 114.82: 2218 114.82 - 121.60: 1896 121.60 - 128.38: 969 128.38 - 135.16: 28 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 2.440 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.368 2.440 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.369 2.440 nonbonded pdb=" OD1 ASP r 314 " pdb=" OG SER r 316 " model vdw 2.369 2.440 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.369 2.440 ... (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 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 '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: 0.770 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: 3.690 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.710 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.660 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.512 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: 0.2572 time to fit residues: 31.0606 Evaluate side-chains 82 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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: 8.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4081 Z= 0.242 Angle : 0.771 12.334 5460 Z= 0.383 Chirality : 0.052 0.137 616 Planarity : 0.003 0.029 693 Dihedral : 7.674 22.601 539 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 1.30 % Allowed : 13.20 % Favored : 85.50 % 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 (0.29), 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 A 362 PHE 0.006 0.001 PHE A 346 TYR 0.009 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 110 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: r 369 LYS cc_start: 0.8528 (mttt) cc_final: 0.8122 (mtpp) REVERT: A 311 LYS cc_start: 0.8507 (tttm) cc_final: 0.8203 (ttmt) REVERT: A 315 LEU cc_start: 0.8936 (tt) cc_final: 0.8724 (mp) REVERT: A 316 SER cc_start: 0.8885 (p) cc_final: 0.8435 (p) REVERT: A 331 LYS cc_start: 0.9010 (mtpt) cc_final: 0.7787 (tptp) REVERT: A 340 LYS cc_start: 0.8747 (mttt) cc_final: 0.8501 (mptt) REVERT: B 311 LYS cc_start: 0.8634 (tttm) cc_final: 0.8333 (ttmt) REVERT: B 336 GLN cc_start: 0.9021 (tt0) cc_final: 0.8814 (tt0) REVERT: D 311 LYS cc_start: 0.8714 (tttm) cc_final: 0.8433 (ttmt) REVERT: E 311 LYS cc_start: 0.8510 (tttt) cc_final: 0.8230 (ttmt) outliers start: 6 outliers final: 3 residues processed: 107 average time/residue: 0.2688 time to fit residues: 32.8406 Evaluate side-chains 86 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain E residue 320 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4081 Z= 0.217 Angle : 0.651 13.763 5460 Z= 0.330 Chirality : 0.051 0.127 616 Planarity : 0.003 0.037 693 Dihedral : 6.758 20.358 539 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.87 % Allowed : 17.32 % Favored : 81.82 % 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: -2.53 (0.30), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 374 PHE 0.004 0.001 PHE E 346 TYR 0.010 0.002 TYR r 310 ARG 0.003 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 91 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8514 (tttm) cc_final: 0.8224 (ttmt) REVERT: A 331 LYS cc_start: 0.9010 (mtpt) cc_final: 0.7846 (tptp) REVERT: A 340 LYS cc_start: 0.8806 (mttt) cc_final: 0.8550 (mptt) REVERT: B 311 LYS cc_start: 0.8519 (tttm) cc_final: 0.8289 (ttmt) REVERT: D 311 LYS cc_start: 0.8727 (tttm) cc_final: 0.8502 (ttmt) REVERT: F 316 SER cc_start: 0.8843 (p) cc_final: 0.8564 (p) REVERT: F 372 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8328 (mm-30) outliers start: 4 outliers final: 4 residues processed: 88 average time/residue: 0.2441 time to fit residues: 25.0631 Evaluate side-chains 90 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4081 Z= 0.264 Angle : 0.608 5.275 5460 Z= 0.321 Chirality : 0.050 0.128 616 Planarity : 0.004 0.035 693 Dihedral : 6.582 18.995 539 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.60 % Allowed : 16.67 % Favored : 80.74 % 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: -2.55 (0.31), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (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 r 346 TYR 0.012 0.003 TYR B 310 ARG 0.003 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 103 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8513 (tttm) cc_final: 0.8253 (ttmt) REVERT: A 331 LYS cc_start: 0.9006 (mtpt) cc_final: 0.8021 (tmtt) REVERT: A 340 LYS cc_start: 0.8821 (mttt) cc_final: 0.8564 (mmtm) REVERT: A 343 LYS cc_start: 0.7793 (ptmm) cc_final: 0.6018 (tppt) REVERT: B 311 LYS cc_start: 0.8537 (tttm) cc_final: 0.8321 (ttmt) REVERT: B 340 LYS cc_start: 0.8974 (mttt) cc_final: 0.8758 (mptt) REVERT: D 311 LYS cc_start: 0.8704 (tttm) cc_final: 0.8491 (ttmt) outliers start: 12 outliers final: 8 residues processed: 98 average time/residue: 0.2387 time to fit residues: 27.2710 Evaluate side-chains 94 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E 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 35 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 0 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4081 Z= 0.308 Angle : 0.629 7.271 5460 Z= 0.331 Chirality : 0.051 0.132 616 Planarity : 0.004 0.040 693 Dihedral : 6.522 21.446 539 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.60 % Allowed : 17.53 % Favored : 79.87 % 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: -2.62 (0.31), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (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 E 346 TYR 0.014 0.004 TYR B 310 ARG 0.004 0.000 ARG r 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 101 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8526 (tttm) cc_final: 0.8266 (ttmt) REVERT: A 331 LYS cc_start: 0.9008 (mtpt) cc_final: 0.7943 (tmtt) REVERT: A 340 LYS cc_start: 0.8848 (mttt) cc_final: 0.8570 (mmtm) REVERT: A 343 LYS cc_start: 0.7813 (ptmm) cc_final: 0.6081 (tppt) REVERT: B 311 LYS cc_start: 0.8605 (tttm) cc_final: 0.8394 (ttmt) REVERT: B 340 LYS cc_start: 0.8997 (mttt) cc_final: 0.8778 (mptt) REVERT: D 311 LYS cc_start: 0.8695 (tttm) cc_final: 0.8448 (ttmt) outliers start: 12 outliers final: 7 residues processed: 91 average time/residue: 0.2428 time to fit residues: 25.6696 Evaluate side-chains 94 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.0470 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 overall best weight: 3.3284 ------------------------------------------------------------------------------- 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 D 336 GLN ** E 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3960 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= 0.299 Angle : 0.621 6.902 5460 Z= 0.325 Chirality : 0.050 0.130 616 Planarity : 0.004 0.043 693 Dihedral : 6.362 20.579 539 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.38 % Allowed : 18.61 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.31), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (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 F 346 TYR 0.013 0.003 TYR C 310 ARG 0.004 0.000 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 105 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8536 (tttm) cc_final: 0.8256 (ttmt) REVERT: A 331 LYS cc_start: 0.9015 (mtpt) cc_final: 0.7993 (tmtt) REVERT: A 340 LYS cc_start: 0.8845 (mttt) cc_final: 0.8567 (mmtm) REVERT: A 343 LYS cc_start: 0.7812 (ptmm) cc_final: 0.6045 (tppt) REVERT: B 311 LYS cc_start: 0.8612 (tttm) cc_final: 0.8404 (ttmt) REVERT: D 311 LYS cc_start: 0.8677 (tttm) cc_final: 0.8432 (ttmt) REVERT: F 372 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8483 (mm-30) outliers start: 11 outliers final: 7 residues processed: 97 average time/residue: 0.2219 time to fit residues: 25.3496 Evaluate side-chains 98 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 372 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.0020 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- 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 E 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 4081 Z= 0.116 Angle : 0.515 6.379 5460 Z= 0.266 Chirality : 0.049 0.126 616 Planarity : 0.003 0.042 693 Dihedral : 5.590 18.933 539 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.16 % Allowed : 18.83 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.32), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.004 0.001 PHE r 346 TYR 0.004 0.001 TYR r 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 116 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9024 (mtpt) cc_final: 0.7909 (tmtt) REVERT: A 340 LYS cc_start: 0.8908 (mttt) cc_final: 0.8638 (mmtm) REVERT: A 345 ASP cc_start: 0.8415 (t0) cc_final: 0.8178 (t0) REVERT: B 340 LYS cc_start: 0.9069 (mttt) cc_final: 0.8866 (mptt) REVERT: B 359 ASN cc_start: 0.8730 (m-40) cc_final: 0.8341 (m-40) outliers start: 10 outliers final: 8 residues processed: 108 average time/residue: 0.2263 time to fit residues: 28.5458 Evaluate side-chains 107 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 358 ASP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 42 optimal weight: 0.3980 chunk 45 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4081 Z= 0.203 Angle : 0.586 8.049 5460 Z= 0.301 Chirality : 0.049 0.121 616 Planarity : 0.004 0.040 693 Dihedral : 5.658 18.851 539 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.16 % Allowed : 19.70 % 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: -2.62 (0.32), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 374 PHE 0.005 0.001 PHE r 346 TYR 0.010 0.002 TYR B 310 ARG 0.002 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 105 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9049 (mtpt) cc_final: 0.7874 (tptt) REVERT: A 340 LYS cc_start: 0.8846 (mttt) cc_final: 0.8576 (mmtm) REVERT: A 343 LYS cc_start: 0.7834 (ptmm) cc_final: 0.6022 (tppt) REVERT: A 345 ASP cc_start: 0.8438 (t0) cc_final: 0.8189 (t0) REVERT: B 359 ASN cc_start: 0.8873 (m-40) cc_final: 0.8487 (m-40) REVERT: C 353 LYS cc_start: 0.8643 (mtpt) cc_final: 0.8442 (mtpt) REVERT: F 372 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8287 (mm-30) outliers start: 10 outliers final: 7 residues processed: 99 average time/residue: 0.2013 time to fit residues: 23.6522 Evaluate side-chains 103 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain F residue 372 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 43 optimal weight: 0.1980 chunk 28 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4081 Z= 0.228 Angle : 0.590 7.570 5460 Z= 0.305 Chirality : 0.050 0.125 616 Planarity : 0.004 0.043 693 Dihedral : 5.721 18.195 539 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.16 % Allowed : 19.91 % Favored : 77.92 % 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: -2.70 (0.32), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 374 PHE 0.005 0.001 PHE r 346 TYR 0.010 0.003 TYR r 310 ARG 0.002 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 102 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9003 (mtpt) cc_final: 0.7818 (tptt) REVERT: A 340 LYS cc_start: 0.8839 (mttt) cc_final: 0.8569 (mmtm) REVERT: A 343 LYS cc_start: 0.8005 (ptmm) cc_final: 0.6173 (tppt) REVERT: A 345 ASP cc_start: 0.8442 (t0) cc_final: 0.8194 (t0) outliers start: 10 outliers final: 8 residues processed: 95 average time/residue: 0.2154 time to fit residues: 24.2659 Evaluate side-chains 99 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 316 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 0.0670 chunk 41 optimal weight: 9.9990 chunk 11 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4081 Z= 0.114 Angle : 0.524 6.689 5460 Z= 0.265 Chirality : 0.048 0.120 616 Planarity : 0.004 0.041 693 Dihedral : 5.124 16.744 539 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.95 % Allowed : 20.56 % Favored : 77.49 % 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: -2.65 (0.33), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.004 0.001 PHE r 346 TYR 0.005 0.001 TYR r 310 ARG 0.003 0.000 ARG C 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 106 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 331 LYS cc_start: 0.9084 (mtpt) cc_final: 0.7949 (tmtt) REVERT: A 340 LYS cc_start: 0.8909 (mttt) cc_final: 0.8639 (mmtm) REVERT: A 345 ASP cc_start: 0.8422 (t0) cc_final: 0.8205 (t0) REVERT: B 359 ASN cc_start: 0.8747 (m-40) cc_final: 0.8397 (m-40) outliers start: 9 outliers final: 7 residues processed: 100 average time/residue: 0.2016 time to fit residues: 24.3121 Evaluate side-chains 98 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 379 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 = 0.4262 r_free = 0.4262 target = 0.143001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.119992 restraints weight = 4641.198| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.43 r_work: 0.3854 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4081 Z= 0.297 Angle : 0.632 7.330 5460 Z= 0.327 Chirality : 0.050 0.131 616 Planarity : 0.004 0.038 693 Dihedral : 5.721 17.206 539 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.73 % Allowed : 21.65 % Favored : 76.62 % 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: -2.74 (0.32), residues: 511 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 374 PHE 0.006 0.001 PHE r 346 TYR 0.014 0.003 TYR A 310 ARG 0.003 0.000 ARG r 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1429.93 seconds wall clock time: 26 minutes 48.80 seconds (1608.80 seconds total)