Starting phenix.real_space_refine on Sun Mar 10 17:42:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/03_2024/8ore_17121.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/03_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_17121/03_2024/8ore_17121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/03_2024/8ore_17121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/03_2024/8ore_17121.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/03_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-dev-5265/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: 2.07, per 1000 atoms: 0.57 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: 2.59 Conformation dependent library (CDL) restraints added in 368.3 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: 0.35 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: 1.11 Time building geometry restraints manager: 2.73 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: 1439 13.53 - 27.06: 117 27.06 - 40.59: 35 40.59 - 54.12: 28 54.12 - 67.65: 52 Dihedral angle restraints: 1671 sinusoidal: 960 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 1668 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: 0.990 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: 3.520 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.320 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.600 ------------------------------------------------------------------------------- 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 : 0.276 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: 2.5970 time to fit residues: 215.9218 Evaluate side-chains 52 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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: 3.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 A 374 HIS B 307 GLN B 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1797 Z= 0.187 Angle : 0.700 4.637 2400 Z= 0.361 Chirality : 0.055 0.150 267 Planarity : 0.004 0.037 306 Dihedral : 7.199 22.649 237 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.15 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: -2.15 (0.47), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.011 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 73 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8524 (m) cc_final: 0.8096 (p) REVERT: A 345 ASP cc_start: 0.8196 (t0) cc_final: 0.7890 (t0) REVERT: B 317 LYS cc_start: 0.7836 (ptmt) cc_final: 0.7289 (ptpp) REVERT: B 319 THR cc_start: 0.8123 (m) cc_final: 0.7619 (p) REVERT: C 314 ASP cc_start: 0.8471 (t0) cc_final: 0.8125 (t0) REVERT: C 380 GLU cc_start: 0.5377 (mt-10) cc_final: 0.5117 (mt-10) outliers start: 10 outliers final: 3 residues processed: 67 average time/residue: 2.2907 time to fit residues: 156.0457 Evaluate side-chains 52 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 377 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN C 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1797 Z= 0.187 Angle : 0.647 5.412 2400 Z= 0.330 Chirality : 0.053 0.149 267 Planarity : 0.004 0.042 306 Dihedral : 6.425 20.203 237 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.48 % Allowed : 25.37 % 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: -2.03 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.014 0.002 PHE A 378 TYR 0.007 0.001 TYR C 310 ARG 0.006 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 54 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.355 Fit side-chains REVERT: A 316 SER cc_start: 0.8610 (m) cc_final: 0.8277 (p) REVERT: A 345 ASP cc_start: 0.8145 (t0) cc_final: 0.7872 (t0) REVERT: A 372 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6555 (tt0) REVERT: B 319 THR cc_start: 0.8176 (m) cc_final: 0.7594 (p) REVERT: B 345 ASP cc_start: 0.7696 (t0) cc_final: 0.7268 (t70) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 1.9027 time to fit residues: 101.0793 Evaluate side-chains 54 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 316 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 316 SER 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: 2.9990 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.0770 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN B 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1797 Z= 0.228 Angle : 0.636 4.934 2400 Z= 0.325 Chirality : 0.053 0.158 267 Planarity : 0.005 0.046 306 Dihedral : 6.345 22.155 237 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 4.98 % Allowed : 23.38 % 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: -1.92 (0.49), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.011 0.002 PHE A 378 TYR 0.006 0.001 TYR C 310 ARG 0.004 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 : 0.277 Fit side-chains revert: symmetry clash REVERT: A 316 SER cc_start: 0.8658 (m) cc_final: 0.8335 (p) REVERT: A 345 ASP cc_start: 0.8187 (t0) cc_final: 0.7920 (t0) REVERT: A 372 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6522 (tt0) REVERT: B 319 THR cc_start: 0.8183 (m) cc_final: 0.7609 (p) REVERT: B 345 ASP cc_start: 0.7679 (t0) cc_final: 0.7169 (t70) REVERT: C 345 ASP cc_start: 0.7907 (t0) cc_final: 0.7418 (t70) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 2.0443 time to fit residues: 112.5189 Evaluate side-chains 52 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 274 LYS 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: 6.9990 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.0570 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- 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: 0.7607 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1797 Z= 0.137 Angle : 0.568 4.366 2400 Z= 0.285 Chirality : 0.052 0.128 267 Planarity : 0.004 0.033 306 Dihedral : 5.698 18.220 237 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 5.47 % Allowed : 22.39 % Favored : 72.14 % 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 (0.49), 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 0.008 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 60 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8643 (m) cc_final: 0.8393 (p) REVERT: A 345 ASP cc_start: 0.8173 (t0) cc_final: 0.7903 (t0) REVERT: A 372 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6684 (tt0) REVERT: B 315 LEU cc_start: 0.8323 (mp) cc_final: 0.8071 (mm) REVERT: B 319 THR cc_start: 0.8179 (m) cc_final: 0.7641 (p) REVERT: B 345 ASP cc_start: 0.7650 (t0) cc_final: 0.7126 (t70) REVERT: C 345 ASP cc_start: 0.7875 (t0) cc_final: 0.7396 (t70) REVERT: C 349 ARG cc_start: 0.7998 (ttp-110) cc_final: 0.7221 (mtp180) REVERT: C 380 GLU cc_start: 0.6536 (tm-30) cc_final: 0.5568 (mt-10) outliers start: 11 outliers final: 7 residues processed: 55 average time/residue: 1.9071 time to fit residues: 107.0869 Evaluate side-chains 55 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain C residue 377 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1797 Z= 0.147 Angle : 0.565 4.282 2400 Z= 0.281 Chirality : 0.052 0.130 267 Planarity : 0.003 0.032 306 Dihedral : 5.453 18.161 237 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.98 % Allowed : 23.88 % Favored : 72.14 % 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: -1.76 (0.49), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (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 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 56 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8633 (m) cc_final: 0.8428 (p) REVERT: A 345 ASP cc_start: 0.8158 (t0) cc_final: 0.7906 (t0) REVERT: A 372 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7156 (tt0) REVERT: B 315 LEU cc_start: 0.8338 (mp) cc_final: 0.8068 (mm) REVERT: B 319 THR cc_start: 0.8191 (m) cc_final: 0.7649 (p) REVERT: B 345 ASP cc_start: 0.7641 (t0) cc_final: 0.7122 (t70) REVERT: C 345 ASP cc_start: 0.7829 (t0) cc_final: 0.7370 (t70) REVERT: C 349 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7268 (mtp180) outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 2.1037 time to fit residues: 107.2104 Evaluate side-chains 53 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain C residue 349 ARG 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: 0.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 0.0970 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.7618 moved from start: 0.6178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1797 Z= 0.175 Angle : 0.578 4.562 2400 Z= 0.289 Chirality : 0.052 0.139 267 Planarity : 0.003 0.034 306 Dihedral : 5.413 17.760 237 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.99 % Allowed : 25.37 % 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: -1.73 (0.49), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.009 0.002 PHE C 378 TYR 0.005 0.001 TYR C 310 ARG 0.001 0.000 ARG B 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 56 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8624 (m) cc_final: 0.8394 (p) REVERT: A 345 ASP cc_start: 0.8150 (t0) cc_final: 0.7883 (t0) REVERT: A 372 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7152 (tt0) REVERT: B 315 LEU cc_start: 0.8349 (mp) cc_final: 0.8077 (mm) REVERT: B 319 THR cc_start: 0.8199 (m) cc_final: 0.7678 (p) REVERT: B 345 ASP cc_start: 0.7614 (t0) cc_final: 0.7084 (t70) REVERT: C 345 ASP cc_start: 0.7817 (t0) cc_final: 0.7343 (t70) REVERT: C 349 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7225 (mtp180) outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 2.0649 time to fit residues: 105.2521 Evaluate side-chains 54 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 372 GLU 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: 5.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.0870 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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: 0.7594 moved from start: 0.6359 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= 0.145 Angle : 0.554 4.035 2400 Z= 0.276 Chirality : 0.051 0.125 267 Planarity : 0.003 0.030 306 Dihedral : 5.179 17.167 237 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.49 % Allowed : 25.87 % 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: -1.75 (0.50), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (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 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 55 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: B 315 LEU cc_start: 0.8363 (mp) cc_final: 0.8102 (mm) REVERT: B 319 THR cc_start: 0.8305 (m) cc_final: 0.7785 (p) REVERT: B 345 ASP cc_start: 0.7525 (t0) cc_final: 0.6956 (t70) REVERT: C 345 ASP cc_start: 0.7792 (t0) cc_final: 0.7312 (t70) REVERT: C 349 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7232 (mtp180) outliers start: 5 outliers final: 2 residues processed: 50 average time/residue: 2.0723 time to fit residues: 105.6189 Evaluate side-chains 51 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 372 GLU 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: 2.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.7938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.6460 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= 0.151 Angle : 0.553 4.125 2400 Z= 0.275 Chirality : 0.051 0.125 267 Planarity : 0.003 0.030 306 Dihedral : 5.054 16.116 237 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.99 % Allowed : 27.86 % 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: -1.72 (0.50), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.005 0.001 PHE C 378 TYR 0.004 0.001 TYR C 310 ARG 0.001 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 53 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.309 Fit side-chains REVERT: B 315 LEU cc_start: 0.8362 (mp) cc_final: 0.8107 (mm) REVERT: B 319 THR cc_start: 0.8251 (m) cc_final: 0.7750 (p) REVERT: B 345 ASP cc_start: 0.7548 (t0) cc_final: 0.7019 (t70) REVERT: B 373 THR cc_start: 0.8576 (p) cc_final: 0.8348 (p) REVERT: C 345 ASP cc_start: 0.7788 (t0) cc_final: 0.7308 (t70) REVERT: C 349 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7160 (mtp180) outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 2.0935 time to fit residues: 106.7195 Evaluate side-chains 54 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 372 GLU 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: 0.0870 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 1797 Z= 0.154 Angle : 0.555 4.379 2400 Z= 0.276 Chirality : 0.051 0.126 267 Planarity : 0.003 0.029 306 Dihedral : 4.964 16.803 237 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.99 % Allowed : 28.36 % Favored : 69.65 % 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: -1.73 (0.50), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (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 51 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.305 Fit side-chains REVERT: B 315 LEU cc_start: 0.8361 (mp) cc_final: 0.8103 (mm) REVERT: B 319 THR cc_start: 0.8236 (m) cc_final: 0.7741 (p) REVERT: B 345 ASP cc_start: 0.7515 (t0) cc_final: 0.7019 (t70) REVERT: B 373 THR cc_start: 0.8556 (p) cc_final: 0.8336 (p) REVERT: C 345 ASP cc_start: 0.7788 (t0) cc_final: 0.7304 (t70) REVERT: C 349 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7188 (mtp85) outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 2.0984 time to fit residues: 102.7786 Evaluate side-chains 50 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 372 GLU 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: 4.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.147224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.129006 restraints weight = 6381.264| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 2.02 r_work: 0.3980 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 1797 Z= 0.163 Angle : 0.554 4.268 2400 Z= 0.278 Chirality : 0.051 0.131 267 Planarity : 0.003 0.033 306 Dihedral : 4.995 16.495 237 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.99 % Allowed : 28.36 % Favored : 69.65 % 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: -1.70 (0.50), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.005 0.001 PHE C 378 TYR 0.004 0.001 TYR C 310 ARG 0.002 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3217.44 seconds wall clock time: 56 minutes 53.09 seconds (3413.09 seconds total)