Starting phenix.real_space_refine on Wed Jan 17 14:11:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/01_2024/8ore_17121.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/01_2024/8ore_17121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/01_2024/8ore_17121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/01_2024/8ore_17121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/01_2024/8ore_17121.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/01_2024/8ore_17121.pdb" } resolution = 2.5 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: 5 Type Number sf(0) Gaussians S 3 5.16 5 C 1110 2.51 5 N 327 2.21 5 O 330 1.98 5 H 1845 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 342": "OE1" <-> "OE2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C GLU 380": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 3615 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1205 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "B" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1205 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1205 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 2.21, per 1000 atoms: 0.61 Number of scatterers: 3615 At special positions: 0 Unit cell: (82.84, 81.75, 37.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 O 330 8.00 N 327 7.00 C 1110 6.00 H 1845 1.00 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: 2.63 Conformation dependent library (CDL) restraints added in 725.0 milliseconds 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 402 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 49.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322 Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.612A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE B 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 361 removed outlier: 6.938A pdb=" N SER B 352 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS A 353 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 354 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY A 355 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER C 352 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS B 353 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE C 354 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY B 355 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 377 62 hydrogen bonds defined for protein. 186 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: 1.10 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 1842 1.11 - 1.29: 297 1.29 - 1.46: 490 1.46 - 1.63: 1010 1.63 - 1.81: 3 Bond restraints: 3642 Sorted by residual: bond pdb=" N GLY A 366 " pdb=" H GLY A 366 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE1 HIS A 362 " pdb=" HE1 HIS A 362 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE1 HIS B 362 " pdb=" HE1 HIS B 362 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LEU C 315 " pdb=" H LEU C 315 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LEU B 315 " pdb=" H LEU B 315 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 3637 not shown) Histogram of bond angle deviations from ideal: 97.13 - 103.45: 34 103.45 - 109.78: 3111 109.78 - 116.11: 1610 116.11 - 122.43: 1520 122.43 - 128.76: 367 Bond angle restraints: 6642 Sorted by residual: angle pdb=" C LEU A 325 " pdb=" CA LEU A 325 " pdb=" CB LEU A 325 " ideal model delta sigma weight residual 111.14 119.05 -7.91 1.39e+00 5.18e-01 3.24e+01 angle pdb=" C LEU B 325 " pdb=" CA LEU B 325 " pdb=" CB LEU B 325 " ideal model delta sigma weight residual 111.40 118.42 -7.02 1.29e+00 6.01e-01 2.96e+01 angle pdb=" N PRO B 364 " pdb=" CA PRO B 364 " pdb=" C PRO B 364 " ideal model delta sigma weight residual 113.57 120.57 -7.00 1.31e+00 5.83e-01 2.86e+01 angle pdb=" CB HIS B 362 " pdb=" CG HIS B 362 " pdb=" CD2 HIS B 362 " ideal model delta sigma weight residual 131.20 124.91 6.29 1.30e+00 5.92e-01 2.34e+01 angle pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " pdb=" CG PHE B 346 " ideal model delta sigma weight residual 113.80 118.61 -4.81 1.00e+00 1.00e+00 2.31e+01 ... (remaining 6637 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 13.53: 1430 13.53 - 27.06: 112 27.06 - 40.59: 26 40.59 - 54.12: 7 54.12 - 67.65: 36 Dihedral angle restraints: 1611 sinusoidal: 900 harmonic: 711 Sorted by residual: dihedral pdb=" C LEU A 325 " pdb=" N LEU A 325 " pdb=" CA LEU A 325 " pdb=" CB LEU A 325 " ideal model delta harmonic sigma weight residual -122.60 -138.99 16.39 0 2.50e+00 1.60e-01 4.30e+01 dihedral pdb=" C VAL B 363 " pdb=" N VAL B 363 " pdb=" CA VAL B 363 " pdb=" CB VAL B 363 " ideal model delta harmonic sigma weight residual -122.00 -137.70 15.70 0 2.50e+00 1.60e-01 3.94e+01 dihedral pdb=" C VAL A 363 " pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" CB VAL A 363 " ideal model delta harmonic sigma weight residual -122.00 -136.54 14.54 0 2.50e+00 1.60e-01 3.38e+01 ... (remaining 1608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 200 0.120 - 0.240: 40 0.240 - 0.360: 16 0.360 - 0.479: 9 0.479 - 0.599: 2 Chirality restraints: 267 Sorted by residual: chirality pdb=" CA LEU A 325 " pdb=" N LEU A 325 " pdb=" C LEU A 325 " pdb=" CB LEU A 325 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.97e+00 chirality pdb=" CA PRO B 364 " pdb=" N PRO B 364 " pdb=" C PRO B 364 " pdb=" CB PRO B 364 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" CA VAL B 363 " pdb=" N VAL B 363 " pdb=" C VAL B 363 " pdb=" CB VAL B 363 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.21e+00 ... (remaining 264 not shown) Planarity restraints: 525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 346 " 0.099 2.00e-02 2.50e+03 4.00e-02 4.80e+01 pdb=" CG PHE A 346 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 PHE A 346 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 346 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE A 346 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 346 " -0.020 2.00e-02 2.50e+03 pdb=" CZ PHE A 346 " 0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 346 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 PHE A 346 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 PHE A 346 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 346 " 0.008 2.00e-02 2.50e+03 pdb=" HZ PHE A 346 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 346 " 0.076 2.00e-02 2.50e+03 3.28e-02 3.23e+01 pdb=" CG PHE B 346 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE B 346 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 346 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE B 346 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 346 " -0.024 2.00e-02 2.50e+03 pdb=" CZ PHE B 346 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE B 346 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 PHE B 346 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE B 346 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE B 346 " 0.012 2.00e-02 2.50e+03 pdb=" HZ PHE B 346 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 341 " -0.030 2.00e-02 2.50e+03 5.52e-02 3.05e+01 pdb=" N GLU B 342 " 0.095 2.00e-02 2.50e+03 pdb=" CA GLU B 342 " -0.027 2.00e-02 2.50e+03 pdb=" H GLU B 342 " -0.038 2.00e-02 2.50e+03 ... (remaining 522 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 317 2.21 - 2.81: 6754 2.81 - 3.40: 9317 3.40 - 4.00: 12465 4.00 - 4.60: 17899 Nonbonded interactions: 46752 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.611 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.636 1.850 nonbonded pdb=" HG1 THR A 377 " pdb=" OE1 GLU A 380 " model vdw 1.650 1.850 nonbonded pdb=" HG1 THR C 377 " pdb=" OE2 GLU C 380 " model vdw 1.662 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.675 1.850 ... (remaining 46747 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' } 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: 0.720 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: 0.060 Extract box with map and model: 3.530 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.130 Find NCS groups from input model: 0.140 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:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 : 0.011 0.052 1797 Z= 0.718 Angle : 2.085 10.566 2400 Z= 1.353 Chirality : 0.140 0.599 267 Planarity : 0.011 0.065 306 Dihedral : 10.934 54.560 696 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Cbeta Deviations : 3.48 % 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: -2.10 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS C 362 PHE 0.055 0.024 PHE B 378 TYR 0.040 0.012 TYR B 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8330 (t0) cc_final: 0.8073 (t0) REVERT: A 349 ARG cc_start: 0.8027 (ttp-170) cc_final: 0.7794 (ttp-110) REVERT: B 314 ASP cc_start: 0.8198 (t0) cc_final: 0.7914 (t0) REVERT: B 317 LYS cc_start: 0.7959 (ptmt) cc_final: 0.7384 (ptpp) REVERT: B 347 LYS cc_start: 0.8635 (mttt) cc_final: 0.8389 (mttp) REVERT: C 307 GLN cc_start: 0.7873 (tt0) cc_final: 0.7448 (tt0) REVERT: C 338 GLU cc_start: 0.8150 (tt0) cc_final: 0.7887 (tt0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 2.5205 time to fit residues: 209.6513 Evaluate side-chains 52 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 368 ASN B 307 GLN B 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1797 Z= 0.187 Angle : 0.698 4.683 2400 Z= 0.358 Chirality : 0.054 0.143 267 Planarity : 0.004 0.041 306 Dihedral : 7.283 22.680 237 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.98 % Allowed : 19.90 % Favored : 75.12 % 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: -2.19 (0.47), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.010 0.002 PHE A 378 TYR 0.006 0.002 TYR C 310 ARG 0.007 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8524 (m) cc_final: 0.8079 (p) REVERT: A 345 ASP cc_start: 0.8232 (t0) cc_final: 0.7918 (t0) REVERT: A 372 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6650 (mt-10) REVERT: B 317 LYS cc_start: 0.7835 (ptmt) cc_final: 0.7288 (ptpp) REVERT: B 319 THR cc_start: 0.8246 (m) cc_final: 0.7719 (p) REVERT: C 314 ASP cc_start: 0.8435 (t0) cc_final: 0.8164 (t0) REVERT: C 380 GLU cc_start: 0.5352 (mt-10) cc_final: 0.5075 (mt-10) outliers start: 10 outliers final: 3 residues processed: 66 average time/residue: 2.3117 time to fit residues: 155.0806 Evaluate side-chains 52 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 377 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 374 HIS C 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1797 Z= 0.182 Angle : 0.649 5.410 2400 Z= 0.332 Chirality : 0.054 0.152 267 Planarity : 0.004 0.046 306 Dihedral : 6.438 21.418 237 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.99 % Allowed : 25.87 % Favored : 71.14 % 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: -2.10 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 329 PHE 0.014 0.002 PHE A 378 TYR 0.008 0.001 TYR C 310 ARG 0.007 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.307 Fit side-chains REVERT: A 316 SER cc_start: 0.8661 (m) cc_final: 0.8339 (p) REVERT: A 345 ASP cc_start: 0.8214 (t0) cc_final: 0.7934 (t0) REVERT: B 319 THR cc_start: 0.8172 (m) cc_final: 0.7581 (p) REVERT: B 345 ASP cc_start: 0.7701 (t0) cc_final: 0.7273 (t70) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 1.8977 time to fit residues: 102.6959 Evaluate side-chains 51 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 351 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.0000 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 336 GLN B 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1797 Z= 0.188 Angle : 0.615 4.612 2400 Z= 0.312 Chirality : 0.053 0.148 267 Planarity : 0.005 0.041 306 Dihedral : 6.204 21.621 237 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.98 % Allowed : 23.88 % Favored : 71.14 % 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: -2.01 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.009 0.002 PHE A 378 TYR 0.005 0.001 TYR C 310 ARG 0.006 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 316 SER cc_start: 0.8674 (m) cc_final: 0.8350 (p) REVERT: A 345 ASP cc_start: 0.8170 (t0) cc_final: 0.7885 (t0) REVERT: B 319 THR cc_start: 0.8188 (m) cc_final: 0.7635 (p) REVERT: B 345 ASP cc_start: 0.7688 (t0) cc_final: 0.7177 (t70) REVERT: C 345 ASP cc_start: 0.7885 (t0) cc_final: 0.7403 (t70) outliers start: 10 outliers final: 5 residues processed: 52 average time/residue: 1.9572 time to fit residues: 103.8259 Evaluate side-chains 53 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 351 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1797 Z= 0.133 Angle : 0.558 3.991 2400 Z= 0.279 Chirality : 0.051 0.127 267 Planarity : 0.003 0.033 306 Dihedral : 5.656 18.504 237 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.48 % Allowed : 24.88 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.49), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.007 0.001 PHE C 378 TYR 0.004 0.001 TYR C 310 ARG 0.004 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8636 (m) cc_final: 0.8408 (p) REVERT: A 345 ASP cc_start: 0.8151 (t0) cc_final: 0.7856 (t0) REVERT: A 372 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6892 (tt0) REVERT: B 319 THR cc_start: 0.8237 (m) cc_final: 0.7718 (p) REVERT: B 345 ASP cc_start: 0.7656 (t0) cc_final: 0.7130 (t70) REVERT: B 380 GLU cc_start: 0.5153 (mt-10) cc_final: 0.4472 (mt-10) REVERT: C 345 ASP cc_start: 0.7886 (t0) cc_final: 0.7398 (t70) REVERT: C 349 ARG cc_start: 0.8029 (ttp-110) cc_final: 0.7271 (mtp180) REVERT: C 380 GLU cc_start: 0.6487 (tm-30) cc_final: 0.5637 (mt-10) outliers start: 7 outliers final: 5 residues processed: 52 average time/residue: 1.9637 time to fit residues: 104.2242 Evaluate side-chains 53 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 351 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1797 Z= 0.233 Angle : 0.625 4.935 2400 Z= 0.317 Chirality : 0.053 0.160 267 Planarity : 0.005 0.043 306 Dihedral : 5.964 23.215 237 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.98 % Allowed : 24.88 % Favored : 71.14 % 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: -1.86 (0.49), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 374 PHE 0.011 0.002 PHE A 378 TYR 0.006 0.001 TYR C 310 ARG 0.005 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8638 (m) cc_final: 0.8355 (p) REVERT: A 345 ASP cc_start: 0.8159 (t0) cc_final: 0.7888 (t0) REVERT: A 372 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7168 (tt0) REVERT: B 319 THR cc_start: 0.8198 (m) cc_final: 0.7660 (p) REVERT: B 345 ASP cc_start: 0.7638 (t0) cc_final: 0.7109 (t70) REVERT: C 345 ASP cc_start: 0.7890 (t0) cc_final: 0.7413 (t70) REVERT: C 349 ARG cc_start: 0.7905 (ttp-110) cc_final: 0.7272 (mtp180) outliers start: 8 outliers final: 5 residues processed: 53 average time/residue: 1.9711 time to fit residues: 106.6692 Evaluate side-chains 52 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 351 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 10 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 1797 Z= 0.158 Angle : 0.575 4.036 2400 Z= 0.288 Chirality : 0.051 0.131 267 Planarity : 0.003 0.037 306 Dihedral : 5.545 19.672 237 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.49 % Allowed : 26.37 % Favored : 71.14 % 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: -1.85 (0.49), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.007 0.001 PHE C 378 TYR 0.004 0.001 TYR C 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8671 (m) cc_final: 0.8467 (p) REVERT: B 315 LEU cc_start: 0.8336 (mp) cc_final: 0.8103 (mm) REVERT: B 319 THR cc_start: 0.8259 (m) cc_final: 0.7764 (p) REVERT: B 345 ASP cc_start: 0.7631 (t0) cc_final: 0.7066 (t70) REVERT: C 345 ASP cc_start: 0.7866 (t0) cc_final: 0.7380 (t70) REVERT: C 349 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7242 (mtp180) outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 2.0952 time to fit residues: 104.6729 Evaluate side-chains 52 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 1797 Z= 0.146 Angle : 0.560 3.873 2400 Z= 0.279 Chirality : 0.051 0.125 267 Planarity : 0.004 0.034 306 Dihedral : 5.331 19.502 237 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.99 % Allowed : 26.87 % Favored : 71.14 % 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: -1.80 (0.50), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.007 0.001 PHE A 378 TYR 0.004 0.001 TYR C 310 ARG 0.004 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: B 315 LEU cc_start: 0.8333 (mp) cc_final: 0.8069 (mm) REVERT: B 319 THR cc_start: 0.8257 (m) cc_final: 0.7770 (p) REVERT: B 345 ASP cc_start: 0.7623 (t0) cc_final: 0.7065 (t70) REVERT: C 345 ASP cc_start: 0.7818 (t0) cc_final: 0.7355 (t70) REVERT: C 349 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7279 (mtp180) outliers start: 4 outliers final: 1 residues processed: 50 average time/residue: 2.1935 time to fit residues: 111.7343 Evaluate side-chains 48 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.6426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 1797 Z= 0.153 Angle : 0.556 3.982 2400 Z= 0.279 Chirality : 0.051 0.128 267 Planarity : 0.003 0.034 306 Dihedral : 5.182 16.753 237 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.00 % Allowed : 27.86 % Favored : 71.14 % 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: -1.77 (0.50), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.007 0.001 PHE C 378 TYR 0.004 0.001 TYR C 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7861 (tp30) REVERT: B 319 THR cc_start: 0.8259 (m) cc_final: 0.7791 (p) REVERT: B 345 ASP cc_start: 0.7527 (t0) cc_final: 0.6987 (t70) REVERT: C 345 ASP cc_start: 0.7817 (t0) cc_final: 0.7343 (t70) REVERT: C 349 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7257 (mtp180) outliers start: 2 outliers final: 1 residues processed: 50 average time/residue: 2.1604 time to fit residues: 110.0565 Evaluate side-chains 51 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 1797 Z= 0.163 Angle : 0.562 3.944 2400 Z= 0.281 Chirality : 0.051 0.132 267 Planarity : 0.004 0.036 306 Dihedral : 5.218 18.546 237 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.49 % Allowed : 27.86 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.50), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.006 0.001 PHE C 378 TYR 0.004 0.001 TYR C 310 ARG 0.002 0.000 ARG B 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.8271 (m) cc_final: 0.7798 (p) REVERT: B 345 ASP cc_start: 0.7511 (t0) cc_final: 0.6996 (t70) REVERT: C 345 ASP cc_start: 0.7788 (t0) cc_final: 0.7303 (t70) REVERT: C 349 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7240 (mtp180) outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 2.1022 time to fit residues: 109.2609 Evaluate side-chains 53 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.146101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.127961 restraints weight = 6666.803| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.07 r_work: 0.3962 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.6490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 1797 Z= 0.158 Angle : 0.565 4.365 2400 Z= 0.281 Chirality : 0.051 0.127 267 Planarity : 0.003 0.034 306 Dihedral : 5.078 16.032 237 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.49 % Allowed : 28.36 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.51), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.007 0.001 PHE C 378 TYR 0.004 0.001 TYR C 310 ARG 0.003 0.001 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3207.51 seconds wall clock time: 56 minutes 33.16 seconds (3393.16 seconds total)