Starting phenix.real_space_refine on Tue Feb 11 06:29:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sz4_40901/02_2025/8sz4_40901.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sz4_40901/02_2025/8sz4_40901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sz4_40901/02_2025/8sz4_40901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sz4_40901/02_2025/8sz4_40901.map" model { file = "/net/cci-nas-00/data/ceres_data/8sz4_40901/02_2025/8sz4_40901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sz4_40901/02_2025/8sz4_40901.cif" } resolution = 2.86 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= 0.009 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 16 5.16 5 C 1378 2.51 5 N 373 2.21 5 O 395 1.98 5 H 2184 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4346 Number of models: 1 Model: "" Number of chains: 1 Chain: "f" Number of atoms: 4346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 4346 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 6, 'TRANS': 252} Chain breaks: 3 Time building chain proxies: 5.46, per 1000 atoms: 1.26 Number of scatterers: 4346 At special positions: 0 Unit cell: (72.184, 104.409, 58.005, 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 16 16.00 O 395 8.00 N 373 7.00 C 1378 6.00 H 2184 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 290.0 milliseconds 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 498 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 1 sheets defined 54.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'f' and resid 362 through 368 Processing helix chain 'f' and resid 369 through 374 removed outlier: 3.643A pdb=" N GLU f 373 " --> pdb=" O ARG f 369 " (cutoff:3.500A) Processing helix chain 'f' and resid 380 through 397 Processing helix chain 'f' and resid 406 through 418 removed outlier: 4.081A pdb=" N ILE f 412 " --> pdb=" O ALA f 408 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS f 418 " --> pdb=" O LYS f 414 " (cutoff:3.500A) Processing helix chain 'f' and resid 420 through 435 Processing helix chain 'f' and resid 464 through 472 removed outlier: 3.551A pdb=" N GLY f 469 " --> pdb=" O ARG f 465 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG f 470 " --> pdb=" O GLU f 466 " (cutoff:3.500A) Processing helix chain 'f' and resid 472 through 485 removed outlier: 4.231A pdb=" N TYR f 485 " --> pdb=" O ILE f 481 " (cutoff:3.500A) Processing helix chain 'f' and resid 600 through 602 No H-bonds generated for 'chain 'f' and resid 600 through 602' Processing helix chain 'f' and resid 609 through 624 Processing helix chain 'f' and resid 652 through 689 removed outlier: 4.109A pdb=" N ARG f 657 " --> pdb=" O PRO f 653 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE f 672 " --> pdb=" O SER f 668 " (cutoff:3.500A) Proline residue: f 682 - end of helix Processing sheet with id=AA1, first strand: chain 'f' and resid 563 through 566 removed outlier: 4.182A pdb=" N TYR f 563 " --> pdb=" O TRP f 552 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 333 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: 1.42 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 2181 1.03 - 1.22: 5 1.22 - 1.42: 902 1.42 - 1.61: 1266 1.61 - 1.81: 29 Bond restraints: 4383 Sorted by residual: bond pdb=" CA GLY f 397 " pdb=" C GLY f 397 " ideal model delta sigma weight residual 1.524 1.508 0.016 1.33e-02 5.65e+03 1.43e+00 bond pdb=" N VAL f 596 " pdb=" CA VAL f 596 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.17e+00 bond pdb=" N GLU f 491 " pdb=" CA GLU f 491 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 6.63e-01 bond pdb=" CB LYS f 675 " pdb=" CG LYS f 675 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.21e-01 bond pdb=" N GLY f 397 " pdb=" CA GLY f 397 " ideal model delta sigma weight residual 1.460 1.451 0.010 1.26e-02 6.30e+03 6.12e-01 ... (remaining 4378 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.25: 7921 6.25 - 12.50: 1 12.50 - 18.75: 0 18.75 - 25.00: 0 25.00 - 31.25: 5 Bond angle restraints: 7927 Sorted by residual: angle pdb=" CG ARG f 467 " pdb=" CB ARG f 467 " pdb=" HB2 ARG f 467 " ideal model delta sigma weight residual 108.00 76.75 31.25 3.00e+00 1.11e-01 1.09e+02 angle pdb=" CA ARG f 467 " pdb=" CB ARG f 467 " pdb=" HB3 ARG f 467 " ideal model delta sigma weight residual 109.00 80.45 28.55 3.00e+00 1.11e-01 9.06e+01 angle pdb=" CG ARG f 467 " pdb=" CB ARG f 467 " pdb=" HB3 ARG f 467 " ideal model delta sigma weight residual 108.00 80.80 27.20 3.00e+00 1.11e-01 8.22e+01 angle pdb=" CA ARG f 467 " pdb=" CB ARG f 467 " pdb=" HB2 ARG f 467 " ideal model delta sigma weight residual 109.00 81.84 27.16 3.00e+00 1.11e-01 8.20e+01 angle pdb=" HB2 ARG f 467 " pdb=" CB ARG f 467 " pdb=" HB3 ARG f 467 " ideal model delta sigma weight residual 110.00 136.12 -26.12 3.00e+00 1.11e-01 7.58e+01 ... (remaining 7922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 1929 15.58 - 31.16: 64 31.16 - 46.74: 17 46.74 - 62.33: 12 62.33 - 77.91: 1 Dihedral angle restraints: 2023 sinusoidal: 1123 harmonic: 900 Sorted by residual: dihedral pdb=" CA GLU f 368 " pdb=" C GLU f 368 " pdb=" N ARG f 369 " pdb=" CA ARG f 369 " ideal model delta harmonic sigma weight residual 180.00 163.24 16.76 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA MET f 651 " pdb=" C MET f 651 " pdb=" N ASP f 652 " pdb=" CA ASP f 652 " ideal model delta harmonic sigma weight residual -180.00 -165.00 -15.00 0 5.00e+00 4.00e-02 9.01e+00 dihedral pdb=" CA ILE f 585 " pdb=" C ILE f 585 " pdb=" N PHE f 586 " pdb=" CA PHE f 586 " ideal model delta harmonic sigma weight residual 180.00 165.48 14.52 0 5.00e+00 4.00e-02 8.44e+00 ... (remaining 2020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 163 0.025 - 0.049: 101 0.049 - 0.074: 39 0.074 - 0.098: 9 0.098 - 0.123: 9 Chirality restraints: 321 Sorted by residual: chirality pdb=" CA ILE f 528 " pdb=" N ILE f 528 " pdb=" C ILE f 528 " pdb=" CB ILE f 528 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA VAL f 544 " pdb=" N VAL f 544 " pdb=" C VAL f 544 " pdb=" CB VAL f 544 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.61e-01 chirality pdb=" CA PRO f 423 " pdb=" N PRO f 423 " pdb=" C PRO f 423 " pdb=" CB PRO f 423 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.13e-01 ... (remaining 318 not shown) Planarity restraints: 622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE f 370 " -0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO f 371 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO f 371 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO f 371 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET f 681 " -0.015 5.00e-02 4.00e+02 2.29e-02 8.36e-01 pdb=" N PRO f 682 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO f 682 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO f 682 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE f 370 " -0.009 2.00e-02 2.50e+03 4.74e-03 6.75e-01 pdb=" CG PHE f 370 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE f 370 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE f 370 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE f 370 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE f 370 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE f 370 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE f 370 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE f 370 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE f 370 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE f 370 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE f 370 " -0.000 2.00e-02 2.50e+03 ... (remaining 619 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 192 2.20 - 2.80: 9080 2.80 - 3.40: 11378 3.40 - 4.00: 14467 4.00 - 4.60: 22546 Nonbonded interactions: 57663 Sorted by model distance: nonbonded pdb=" O ASN f 569 " pdb="HD21 ASN f 590 " model vdw 1.604 2.450 nonbonded pdb=" HB2 ARG f 467 " pdb=" HG2 ARG f 467 " model vdw 1.647 1.952 nonbonded pdb=" OD2 ASP f 599 " pdb=" H GLN f 602 " model vdw 1.648 2.450 nonbonded pdb=" OD1 ASP f 568 " pdb=" H ASN f 569 " model vdw 1.648 2.450 nonbonded pdb=" OD1 ASP f 555 " pdb=" H ASP f 556 " model vdw 1.680 2.450 ... (remaining 57658 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 9.650 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: 0.080 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.320 Find NCS groups from input model: 0.030 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:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2658 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 : 0.003 0.026 2199 Z= 0.214 Angle : 0.572 10.160 2947 Z= 0.333 Chirality : 0.038 0.123 321 Planarity : 0.003 0.033 373 Dihedral : 9.743 77.906 855 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.54), residues: 251 helix: 0.18 (0.49), residues: 122 sheet: 0.51 (0.88), residues: 40 loop : -1.24 (0.62), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP f 552 HIS 0.003 0.001 HIS f 396 PHE 0.014 0.001 PHE f 370 TYR 0.007 0.001 TYR f 485 ARG 0.002 0.000 ARG f 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 361 ARG cc_start: 0.3936 (tpt90) cc_final: 0.3287 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 2.1137 time to fit residues: 103.8968 Evaluate side-chains 42 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.0570 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 12 optimal weight: 0.0370 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 overall best weight: 0.1374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 569 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.286033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.236500 restraints weight = 7934.746| |-----------------------------------------------------------------------------| r_work (start): 0.4503 rms_B_bonded: 3.45 r_work: 0.4294 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4207 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2199 Z= 0.214 Angle : 0.632 9.457 2947 Z= 0.344 Chirality : 0.040 0.134 321 Planarity : 0.004 0.029 373 Dihedral : 4.359 14.440 282 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.35 % Allowed : 6.28 % Favored : 90.38 % 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: 0.66 (0.54), residues: 251 helix: 1.35 (0.46), residues: 130 sheet: 1.13 (0.96), residues: 34 loop : -1.26 (0.65), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP f 542 HIS 0.003 0.001 HIS f 396 PHE 0.016 0.002 PHE f 620 TYR 0.006 0.001 TYR f 485 ARG 0.004 0.001 ARG f 386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 45 average time/residue: 2.2375 time to fit residues: 103.2403 Evaluate side-chains 39 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 400 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 6 optimal weight: 0.2980 chunk 1 optimal weight: 0.0980 chunk 23 optimal weight: 0.2980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 569 ASN f 658 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.282192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.237180 restraints weight = 7834.140| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 3.28 r_work: 0.3954 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 2199 Z= 0.343 Angle : 0.710 10.055 2947 Z= 0.377 Chirality : 0.041 0.131 321 Planarity : 0.005 0.038 373 Dihedral : 4.736 18.236 282 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.93 % Allowed : 9.62 % Favored : 87.45 % 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: 0.37 (0.53), residues: 251 helix: 1.22 (0.45), residues: 131 sheet: 0.71 (0.96), residues: 34 loop : -1.48 (0.64), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP f 542 HIS 0.007 0.002 HIS f 687 PHE 0.019 0.002 PHE f 370 TYR 0.012 0.001 TYR f 485 ARG 0.008 0.001 ARG f 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 361 ARG cc_start: 0.7146 (ttp80) cc_final: 0.5178 (ttp80) REVERT: f 368 GLU cc_start: 0.5695 (OUTLIER) cc_final: 0.4859 (mp0) REVERT: f 491 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.5670 (tt0) outliers start: 7 outliers final: 2 residues processed: 39 average time/residue: 1.8882 time to fit residues: 75.9181 Evaluate side-chains 38 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 368 GLU Chi-restraints excluded: chain f residue 400 THR Chi-restraints excluded: chain f residue 491 GLU Chi-restraints excluded: chain f residue 564 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 18 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 8 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 chunk 7 optimal weight: 0.0870 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.0470 overall best weight: 0.2456 ------------------------------------------------------------------------------- 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 = 0.4910 r_free = 0.4910 target = 0.283025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.238280 restraints weight = 7791.574| |-----------------------------------------------------------------------------| r_work (start): 0.4518 rms_B_bonded: 2.94 r_work: 0.4228 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4143 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2199 Z= 0.249 Angle : 0.628 9.761 2947 Z= 0.330 Chirality : 0.039 0.128 321 Planarity : 0.004 0.038 373 Dihedral : 4.563 18.674 282 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.51 % Allowed : 8.37 % Favored : 89.12 % 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: 0.66 (0.53), residues: 251 helix: 1.65 (0.45), residues: 131 sheet: 0.44 (0.94), residues: 34 loop : -1.51 (0.62), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP f 542 HIS 0.004 0.001 HIS f 687 PHE 0.016 0.002 PHE f 370 TYR 0.013 0.001 TYR f 485 ARG 0.003 0.000 ARG f 361 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 361 ARG cc_start: 0.6968 (ttp80) cc_final: 0.5203 (ttt180) REVERT: f 368 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5865 (mp0) REVERT: f 491 GLU cc_start: 0.6302 (OUTLIER) cc_final: 0.5875 (tt0) outliers start: 6 outliers final: 2 residues processed: 37 average time/residue: 1.7510 time to fit residues: 66.8600 Evaluate side-chains 38 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 368 GLU Chi-restraints excluded: chain f residue 400 THR Chi-restraints excluded: chain f residue 491 GLU Chi-restraints excluded: chain f residue 564 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 16 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 8 optimal weight: 0.0670 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 overall best weight: 0.2276 ------------------------------------------------------------------------------- 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 = 0.4916 r_free = 0.4916 target = 0.283662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.241156 restraints weight = 7900.918| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 2.92 r_work: 0.4099 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3996 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2199 Z= 0.244 Angle : 0.621 9.741 2947 Z= 0.327 Chirality : 0.039 0.126 321 Planarity : 0.004 0.038 373 Dihedral : 4.540 17.060 282 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.51 % Allowed : 9.21 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.53), residues: 251 helix: 1.90 (0.45), residues: 131 sheet: 0.32 (0.94), residues: 34 loop : -1.61 (0.62), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP f 542 HIS 0.003 0.001 HIS f 687 PHE 0.015 0.002 PHE f 370 TYR 0.013 0.002 TYR f 485 ARG 0.004 0.000 ARG f 364 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 361 ARG cc_start: 0.6935 (ttp80) cc_final: 0.4187 (tpp80) REVERT: f 368 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.5512 (mp0) REVERT: f 491 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5939 (tt0) outliers start: 6 outliers final: 2 residues processed: 37 average time/residue: 1.8252 time to fit residues: 69.6671 Evaluate side-chains 38 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 368 GLU Chi-restraints excluded: chain f residue 400 THR Chi-restraints excluded: chain f residue 491 GLU Chi-restraints excluded: chain f residue 564 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 0.0570 chunk 24 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.0570 chunk 23 optimal weight: 0.2980 chunk 5 optimal weight: 0.0670 chunk 2 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.1354 ------------------------------------------------------------------------------- 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 = 0.4919 r_free = 0.4919 target = 0.283718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.238804 restraints weight = 7710.705| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 2.96 r_work: 0.4210 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4119 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2199 Z= 0.172 Angle : 0.563 9.596 2947 Z= 0.295 Chirality : 0.037 0.123 321 Planarity : 0.003 0.036 373 Dihedral : 4.244 15.440 282 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.67 % Allowed : 10.88 % Favored : 87.45 % 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: 1.17 (0.54), residues: 251 helix: 2.45 (0.45), residues: 131 sheet: 0.00 (0.99), residues: 28 loop : -1.56 (0.60), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP f 542 HIS 0.002 0.001 HIS f 584 PHE 0.013 0.001 PHE f 370 TYR 0.009 0.001 TYR f 485 ARG 0.002 0.000 ARG f 386 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 361 ARG cc_start: 0.6923 (ttp80) cc_final: 0.4019 (tpp80) REVERT: f 491 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.5953 (tt0) outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 1.7221 time to fit residues: 67.5053 Evaluate side-chains 36 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 400 THR Chi-restraints excluded: chain f residue 491 GLU Chi-restraints excluded: chain f residue 564 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 5 optimal weight: 0.2980 chunk 2 optimal weight: 0.2980 chunk 6 optimal weight: 0.1980 chunk 1 optimal weight: 0.0670 chunk 19 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.0270 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 0.1980 overall best weight: 0.1576 ------------------------------------------------------------------------------- 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 = 0.4926 r_free = 0.4926 target = 0.284970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.243833 restraints weight = 7747.618| |-----------------------------------------------------------------------------| r_work (start): 0.4524 rms_B_bonded: 2.90 r_work: 0.4242 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4156 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2199 Z= 0.190 Angle : 0.580 9.717 2947 Z= 0.303 Chirality : 0.037 0.123 321 Planarity : 0.003 0.035 373 Dihedral : 4.226 14.789 282 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.09 % Allowed : 10.46 % Favored : 87.45 % 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: 1.36 (0.55), residues: 251 helix: 2.66 (0.46), residues: 131 sheet: -0.04 (0.98), residues: 28 loop : -1.52 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP f 542 HIS 0.002 0.001 HIS f 584 PHE 0.013 0.001 PHE f 370 TYR 0.011 0.001 TYR f 485 ARG 0.002 0.000 ARG f 364 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 361 ARG cc_start: 0.6951 (ttp80) cc_final: 0.4086 (tpp80) REVERT: f 399 ARG cc_start: 0.7591 (mtm180) cc_final: 0.6473 (mpt90) REVERT: f 491 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.5928 (tt0) REVERT: f 651 MET cc_start: 0.4900 (pmt) cc_final: 0.4657 (pmt) outliers start: 5 outliers final: 3 residues processed: 38 average time/residue: 1.8788 time to fit residues: 73.5234 Evaluate side-chains 39 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 400 THR Chi-restraints excluded: chain f residue 432 ILE Chi-restraints excluded: chain f residue 491 GLU Chi-restraints excluded: chain f residue 564 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 0.1980 chunk 2 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 23 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.1980 overall best weight: 0.1776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 569 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.285445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.242943 restraints weight = 7727.291| |-----------------------------------------------------------------------------| r_work (start): 0.4496 rms_B_bonded: 2.69 r_work: 0.4223 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4137 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2199 Z= 0.201 Angle : 0.592 9.777 2947 Z= 0.308 Chirality : 0.037 0.122 321 Planarity : 0.003 0.035 373 Dihedral : 4.237 16.400 282 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.67 % Allowed : 10.46 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.55), residues: 251 helix: 2.60 (0.45), residues: 131 sheet: 0.08 (1.01), residues: 28 loop : -1.50 (0.62), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP f 542 HIS 0.002 0.001 HIS f 687 PHE 0.014 0.001 PHE f 370 TYR 0.011 0.001 TYR f 485 ARG 0.002 0.000 ARG f 364 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 361 ARG cc_start: 0.6936 (ttp80) cc_final: 0.4132 (tpp80) REVERT: f 399 ARG cc_start: 0.7673 (mtm180) cc_final: 0.6510 (mpt90) REVERT: f 491 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.5922 (tt0) REVERT: f 651 MET cc_start: 0.4714 (pmt) cc_final: 0.4493 (pmt) outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 2.0353 time to fit residues: 79.4502 Evaluate side-chains 37 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 400 THR Chi-restraints excluded: chain f residue 491 GLU Chi-restraints excluded: chain f residue 564 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 4 optimal weight: 0.0970 chunk 2 optimal weight: 0.0970 chunk 1 optimal weight: 0.0980 chunk 3 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.0870 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.0870 chunk 15 optimal weight: 0.7980 overall best weight: 0.0932 ------------------------------------------------------------------------------- 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 = 0.4944 r_free = 0.4944 target = 0.287018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.244472 restraints weight = 7822.977| |-----------------------------------------------------------------------------| r_work (start): 0.4618 rms_B_bonded: 2.71 r_work: 0.4334 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4249 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2199 Z= 0.158 Angle : 0.582 9.611 2947 Z= 0.298 Chirality : 0.037 0.123 321 Planarity : 0.003 0.035 373 Dihedral : 4.057 14.483 282 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.09 % Allowed : 11.72 % Favored : 86.19 % 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: 1.54 (0.56), residues: 251 helix: 2.83 (0.46), residues: 133 sheet: 0.10 (1.02), residues: 28 loop : -1.61 (0.61), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP f 542 HIS 0.001 0.001 HIS f 396 PHE 0.011 0.001 PHE f 370 TYR 0.011 0.002 TYR f 626 ARG 0.002 0.000 ARG f 386 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 361 ARG cc_start: 0.6920 (ttp80) cc_final: 0.4058 (tpp80) REVERT: f 399 ARG cc_start: 0.7509 (mtm180) cc_final: 0.6305 (mpt90) outliers start: 5 outliers final: 3 residues processed: 41 average time/residue: 1.8659 time to fit residues: 78.6929 Evaluate side-chains 38 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 400 THR Chi-restraints excluded: chain f residue 550 LEU Chi-restraints excluded: chain f residue 564 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 0.1980 chunk 1 optimal weight: 0.0870 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 chunk 10 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.0970 chunk 2 optimal weight: 0.0980 overall best weight: 0.1154 ------------------------------------------------------------------------------- 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 = 0.4941 r_free = 0.4941 target = 0.286932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.243620 restraints weight = 7629.688| |-----------------------------------------------------------------------------| r_work (start): 0.4529 rms_B_bonded: 2.69 r_work: 0.4259 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4171 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2199 Z= 0.187 Angle : 0.598 9.908 2947 Z= 0.305 Chirality : 0.037 0.122 321 Planarity : 0.003 0.034 373 Dihedral : 4.027 15.074 282 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.26 % Allowed : 12.55 % Favored : 86.19 % 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: 1.57 (0.56), residues: 251 helix: 2.91 (0.46), residues: 132 sheet: 0.12 (1.03), residues: 28 loop : -1.64 (0.61), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP f 542 HIS 0.002 0.001 HIS f 584 PHE 0.011 0.001 PHE f 370 TYR 0.013 0.002 TYR f 626 ARG 0.006 0.000 ARG f 467 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 361 ARG cc_start: 0.6932 (ttp80) cc_final: 0.4080 (tpp80) REVERT: f 399 ARG cc_start: 0.7624 (mtm180) cc_final: 0.6407 (mpt90) outliers start: 3 outliers final: 3 residues processed: 37 average time/residue: 1.6283 time to fit residues: 62.2448 Evaluate side-chains 38 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 400 THR Chi-restraints excluded: chain f residue 550 LEU Chi-restraints excluded: chain f residue 564 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.0870 chunk 19 optimal weight: 8.9990 chunk 0 optimal weight: 0.1980 chunk 15 optimal weight: 0.3980 chunk 23 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 chunk 22 optimal weight: 0.0570 overall best weight: 0.1074 ------------------------------------------------------------------------------- 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 = 0.4947 r_free = 0.4947 target = 0.287595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.244613 restraints weight = 7768.412| |-----------------------------------------------------------------------------| r_work (start): 0.4541 rms_B_bonded: 2.86 r_work: 0.4267 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4183 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2199 Z= 0.176 Angle : 0.582 9.447 2947 Z= 0.299 Chirality : 0.037 0.122 321 Planarity : 0.003 0.034 373 Dihedral : 3.986 14.970 282 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.67 % Allowed : 12.13 % Favored : 86.19 % 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: 1.62 (0.56), residues: 251 helix: 2.98 (0.46), residues: 132 sheet: 0.12 (1.02), residues: 28 loop : -1.65 (0.60), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP f 542 HIS 0.001 0.001 HIS f 584 PHE 0.013 0.001 PHE f 620 TYR 0.015 0.002 TYR f 626 ARG 0.001 0.000 ARG f 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5761.04 seconds wall clock time: 101 minutes 26.25 seconds (6086.25 seconds total)