Starting phenix.real_space_refine on Thu Mar 6 02:02:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sz4_40901/03_2025/8sz4_40901.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sz4_40901/03_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_40901/03_2025/8sz4_40901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sz4_40901/03_2025/8sz4_40901.map" model { file = "/net/cci-nas-00/data/ceres_data/8sz4_40901/03_2025/8sz4_40901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sz4_40901/03_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-5624/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: 4.71, per 1000 atoms: 1.08 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: 1.38 Conformation dependent library (CDL) restraints added in 295.2 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: 0.36 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: 1.35 Time building geometry restraints manager: 1.41 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: 9.620 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: 0.070 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.580 Find NCS groups from input model: 0.030 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:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.560 ------------------------------------------------------------------------------- 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 : 0.364 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: 2.0584 time to fit residues: 101.2838 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 : 0.325 ------------------------------------------------------------------------------- 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 = 0.236499 restraints weight = 7934.746| |-----------------------------------------------------------------------------| r_work (start): 0.4503 rms_B_bonded: 3.45 r_work: 0.4293 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4208 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 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 : 0.333 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: 2.1055 time to fit residues: 97.0045 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 : 0.321 ------------------------------------------------------------------------------- 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: 0.3980 chunk 20 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 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: 0.2780 ------------------------------------------------------------------------------- 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 = 0.282222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.233188 restraints weight = 7824.768| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 3.70 r_work: 0.4240 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4154 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 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 : 0.005 0.037 2199 Z= 0.296 Angle : 0.681 10.130 2947 Z= 0.362 Chirality : 0.040 0.133 321 Planarity : 0.005 0.037 373 Dihedral : 4.649 17.351 282 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.51 % Allowed : 9.62 % 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: 0.54 (0.54), residues: 251 helix: 1.43 (0.45), residues: 131 sheet: 0.69 (0.96), residues: 34 loop : -1.49 (0.64), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP f 542 HIS 0.006 0.002 HIS f 687 PHE 0.018 0.002 PHE f 370 TYR 0.011 0.001 TYR f 485 ARG 0.005 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 43 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.826 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: 0.7143 (ttp80) cc_final: 0.5004 (ttp80) REVERT: f 368 GLU cc_start: 0.5458 (OUTLIER) cc_final: 0.4860 (mp0) REVERT: f 491 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.5702 (tt0) outliers start: 6 outliers final: 2 residues processed: 41 average time/residue: 2.4512 time to fit residues: 104.2570 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 : 1.485 ------------------------------------------------------------------------------- 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: 2.9990 chunk 8 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.0570 chunk 7 optimal weight: 0.0770 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 overall best weight: 0.2454 ------------------------------------------------------------------------------- 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 = 0.4914 r_free = 0.4914 target = 0.283458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.237938 restraints weight = 7768.856| |-----------------------------------------------------------------------------| r_work (start): 0.4489 rms_B_bonded: 2.81 r_work: 0.4225 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4137 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2199 Z= 0.255 Angle : 0.627 9.808 2947 Z= 0.330 Chirality : 0.039 0.126 321 Planarity : 0.004 0.038 373 Dihedral : 4.534 17.887 282 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.51 % Allowed : 8.79 % Favored : 88.70 % 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: 0.71 (0.53), residues: 251 helix: 1.79 (0.45), residues: 131 sheet: 0.37 (0.94), residues: 34 loop : -1.63 (0.60), 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 0.012 0.001 TYR f 485 ARG 0.004 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 : 0.366 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: 0.7034 (ttp80) cc_final: 0.3939 (ttt-90) REVERT: f 368 GLU cc_start: 0.5641 (OUTLIER) cc_final: 0.5337 (mp0) REVERT: f 491 GLU cc_start: 0.6272 (OUTLIER) cc_final: 0.5850 (tt0) outliers start: 6 outliers final: 2 residues processed: 37 average time/residue: 1.7409 time to fit residues: 66.4802 Evaluate side-chains 37 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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: 10.0000 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 0.0770 chunk 8 optimal weight: 0.0570 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 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 = 0.4917 r_free = 0.4917 target = 0.283621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.240494 restraints weight = 7897.762| |-----------------------------------------------------------------------------| r_work (start): 0.4519 rms_B_bonded: 2.85 r_work: 0.4239 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4153 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2199 Z= 0.257 Angle : 0.632 9.776 2947 Z= 0.332 Chirality : 0.039 0.126 321 Planarity : 0.004 0.038 373 Dihedral : 4.559 17.395 282 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.51 % Allowed : 9.62 % 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: 0.80 (0.53), residues: 251 helix: 1.97 (0.45), residues: 131 sheet: 0.22 (0.93), residues: 34 loop : -1.69 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP f 542 HIS 0.004 0.001 HIS f 687 PHE 0.015 0.002 PHE f 370 TYR 0.014 0.002 TYR f 485 ARG 0.003 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 : 0.333 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: 0.6953 (ttp80) cc_final: 0.4125 (tpp80) REVERT: f 368 GLU cc_start: 0.5689 (OUTLIER) cc_final: 0.5206 (mp0) REVERT: f 491 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.5913 (tt0) outliers start: 6 outliers final: 2 residues processed: 37 average time/residue: 1.6683 time to fit residues: 63.7929 Evaluate side-chains 37 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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: 0.0980 chunk 24 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.0670 chunk 23 optimal weight: 0.3980 chunk 5 optimal weight: 0.0870 chunk 2 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.1496 ------------------------------------------------------------------------------- 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 = 0.285160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.241788 restraints weight = 7730.319| |-----------------------------------------------------------------------------| r_work (start): 0.4443 rms_B_bonded: 2.79 r_work: 0.4110 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.4011 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2199 Z= 0.181 Angle : 0.572 9.652 2947 Z= 0.300 Chirality : 0.037 0.124 321 Planarity : 0.003 0.036 373 Dihedral : 4.300 15.685 282 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.67 % Allowed : 11.72 % Favored : 86.61 % 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: 1.16 (0.54), residues: 251 helix: 2.45 (0.45), residues: 131 sheet: -0.01 (1.00), residues: 28 loop : -1.57 (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 0.010 0.002 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 38 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.436 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: 0.6894 (ttp80) cc_final: 0.4152 (tpp80) REVERT: f 491 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.6048 (tt0) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 1.7174 time to fit residues: 65.7528 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 : 0.381 ------------------------------------------------------------------------------- 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: 0.2980 chunk 1 optimal weight: 0.0670 chunk 19 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 0.1980 overall best weight: 0.2318 ------------------------------------------------------------------------------- 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 = 0.4922 r_free = 0.4922 target = 0.285026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.242524 restraints weight = 7738.406| |-----------------------------------------------------------------------------| r_work (start): 0.4552 rms_B_bonded: 2.96 r_work: 0.4255 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4171 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2199 Z= 0.247 Angle : 0.622 9.920 2947 Z= 0.325 Chirality : 0.038 0.124 321 Planarity : 0.004 0.036 373 Dihedral : 4.402 16.138 282 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.09 % Allowed : 11.30 % Favored : 86.61 % 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: 1.10 (0.54), residues: 251 helix: 2.38 (0.46), residues: 131 sheet: 0.03 (1.01), residues: 28 loop : -1.58 (0.60), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP f 542 HIS 0.003 0.001 HIS f 687 PHE 0.014 0.001 PHE f 370 TYR 0.014 0.002 TYR f 485 ARG 0.003 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 39 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.336 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: 0.6994 (ttp80) cc_final: 0.4144 (tpp80) REVERT: f 368 GLU cc_start: 0.5723 (OUTLIER) cc_final: 0.4925 (mm-30) REVERT: f 491 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.5974 (tt0) REVERT: f 651 MET cc_start: 0.5069 (pmt) cc_final: 0.4844 (pmt) outliers start: 5 outliers final: 2 residues processed: 37 average time/residue: 1.6717 time to fit residues: 63.9063 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 : 0.322 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 0.1980 chunk 2 optimal weight: 0.1980 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 23 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 overall best weight: 0.2380 ------------------------------------------------------------------------------- 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 = 0.4922 r_free = 0.4922 target = 0.284944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.242048 restraints weight = 7700.912| |-----------------------------------------------------------------------------| r_work (start): 0.4461 rms_B_bonded: 2.78 r_work: 0.4077 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3975 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.5260 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= 0.249 Angle : 0.626 9.938 2947 Z= 0.326 Chirality : 0.038 0.123 321 Planarity : 0.004 0.037 373 Dihedral : 4.408 16.187 282 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.09 % Allowed : 10.88 % Favored : 87.03 % 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: 1.07 (0.55), residues: 251 helix: 2.35 (0.46), residues: 131 sheet: 0.11 (1.03), residues: 28 loop : -1.63 (0.61), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP f 542 HIS 0.003 0.001 HIS f 687 PHE 0.014 0.002 PHE f 370 TYR 0.013 0.002 TYR f 485 ARG 0.003 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 38 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.329 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: 0.6998 (ttp80) cc_final: 0.4225 (tpp80) REVERT: f 368 GLU cc_start: 0.5814 (OUTLIER) cc_final: 0.5085 (mm-30) REVERT: f 491 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.6032 (tt0) REVERT: f 651 MET cc_start: 0.5247 (pmt) cc_final: 0.5009 (pmt) outliers start: 5 outliers final: 2 residues processed: 36 average time/residue: 1.7419 time to fit residues: 64.7185 Evaluate side-chains 37 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 10 optimal weight: 0.4980 chunk 7 optimal weight: 0.2980 chunk 4 optimal weight: 0.0670 chunk 2 optimal weight: 0.2980 chunk 1 optimal weight: 0.0370 chunk 3 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.0470 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 overall best weight: 0.0612 ------------------------------------------------------------------------------- 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 = 0.4948 r_free = 0.4948 target = 0.287684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.243995 restraints weight = 7810.602| |-----------------------------------------------------------------------------| r_work (start): 0.4592 rms_B_bonded: 2.66 r_work: 0.4347 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4266 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2199 Z= 0.146 Angle : 0.547 9.453 2947 Z= 0.285 Chirality : 0.036 0.123 321 Planarity : 0.003 0.037 373 Dihedral : 4.024 14.201 282 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.67 % Allowed : 11.72 % Favored : 86.61 % 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: 2.93 (0.47), residues: 133 sheet: 0.11 (1.03), residues: 28 loop : -1.72 (0.60), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP f 542 HIS 0.002 0.001 HIS f 396 PHE 0.010 0.001 PHE f 370 TYR 0.009 0.001 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: 4 poor density : 38 time to evaluate : 0.377 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: 0.6869 (ttp80) cc_final: 0.3998 (tpp80) outliers start: 4 outliers final: 3 residues processed: 41 average time/residue: 1.7457 time to fit residues: 73.8419 Evaluate side-chains 39 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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: 0.3980 chunk 1 optimal weight: 0.0870 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 0.4980 chunk 8 optimal weight: 0.0470 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 chunk 10 optimal weight: 0.0270 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 0.0870 chunk 2 optimal weight: 0.0970 overall best weight: 0.0690 ------------------------------------------------------------------------------- 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 = 0.4951 r_free = 0.4951 target = 0.287785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.244837 restraints weight = 7688.674| |-----------------------------------------------------------------------------| r_work (start): 0.4531 rms_B_bonded: 2.71 r_work: 0.4272 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4185 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2199 Z= 0.170 Angle : 0.596 9.776 2947 Z= 0.301 Chirality : 0.037 0.123 321 Planarity : 0.003 0.035 373 Dihedral : 3.919 13.936 282 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.26 % Allowed : 12.97 % Favored : 85.77 % 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: 2.99 (0.46), residues: 133 sheet: 0.08 (1.01), residues: 28 loop : -1.70 (0.61), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP f 542 HIS 0.002 0.001 HIS f 584 PHE 0.008 0.001 PHE f 370 TYR 0.017 0.001 TYR f 626 ARG 0.005 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 40 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.357 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: 0.6901 (ttp80) cc_final: 0.4030 (tpp80) REVERT: f 399 ARG cc_start: 0.7415 (mtm180) cc_final: 0.6210 (mtt90) outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 1.5876 time to fit residues: 64.0381 Evaluate side-chains 39 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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: 0.9980 chunk 9 optimal weight: 0.1980 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 0.1980 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 overall best weight: 0.1978 ------------------------------------------------------------------------------- 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 = 0.4923 r_free = 0.4923 target = 0.285457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.241542 restraints weight = 7798.884| |-----------------------------------------------------------------------------| r_work (start): 0.4524 rms_B_bonded: 2.64 r_work: 0.4247 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4165 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2199 Z= 0.234 Angle : 0.627 9.812 2947 Z= 0.323 Chirality : 0.038 0.123 321 Planarity : 0.003 0.035 373 Dihedral : 4.170 15.080 282 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.26 % Allowed : 13.39 % Favored : 85.36 % 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: 1.34 (0.55), residues: 251 helix: 2.68 (0.46), residues: 132 sheet: 0.18 (1.01), residues: 28 loop : -1.72 (0.60), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP f 542 HIS 0.002 0.001 HIS f 687 PHE 0.013 0.001 PHE f 370 TYR 0.012 0.002 TYR f 485 ARG 0.003 0.000 ARG f 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6088.78 seconds wall clock time: 105 minutes 17.12 seconds (6317.12 seconds total)