Starting phenix.real_space_refine on Fri Aug 22 14:52:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sz4_40901/08_2025/8sz4_40901.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sz4_40901/08_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_40901/08_2025/8sz4_40901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sz4_40901/08_2025/8sz4_40901.map" model { file = "/net/cci-nas-00/data/ceres_data/8sz4_40901/08_2025/8sz4_40901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sz4_40901/08_2025/8sz4_40901.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.01, per 1000 atoms: 0.23 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: 0.43 Conformation dependent library (CDL) restraints added in 119.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.12 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: 0.84 Time building geometry restraints manager: 0.61 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: 10.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.910 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:7.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.350 ------------------------------------------------------------------------------- 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= 0.162 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG f 467 TYR 0.007 0.001 TYR f 485 PHE 0.014 0.001 PHE f 370 TRP 0.002 0.001 TRP f 552 HIS 0.003 0.001 HIS f 396 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 2199) covalent geometry : angle 0.57244 ( 2947) hydrogen bonds : bond 0.25407 ( 114) hydrogen bonds : angle 7.84215 ( 333) *********************** 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 : 0.114 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: 0.9445 time to fit residues: 46.2982 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 : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.0770 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 8 optimal weight: 0.0470 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.1980 chunk 9 optimal weight: 0.0770 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.0970 overall best weight: 0.0992 ------------------------------------------------------------------------------- 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 = 0.4946 r_free = 0.4946 target = 0.287164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.238812 restraints weight = 8049.211| |-----------------------------------------------------------------------------| r_work (start): 0.4437 rms_B_bonded: 2.46 r_work: 0.4209 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4107 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.2483 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= 0.141 Angle : 0.622 9.405 2947 Z= 0.339 Chirality : 0.039 0.131 321 Planarity : 0.004 0.030 373 Dihedral : 4.272 14.175 282 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.93 % Allowed : 6.28 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.54), residues: 251 helix: 1.48 (0.46), residues: 130 sheet: 1.10 (0.96), residues: 34 loop : -1.27 (0.65), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG f 386 TYR 0.006 0.001 TYR f 485 PHE 0.014 0.002 PHE f 370 TRP 0.006 0.001 TRP f 542 HIS 0.004 0.001 HIS f 396 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 2199) covalent geometry : angle 0.62181 ( 2947) hydrogen bonds : bond 0.07039 ( 114) hydrogen bonds : angle 4.95945 ( 333) *********************** 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 51 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.088 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: 0.6427 (tpt90) cc_final: 0.6138 (ttt-90) outliers start: 7 outliers final: 1 residues processed: 46 average time/residue: 0.9440 time to fit residues: 44.3277 Evaluate side-chains 41 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.071 ------------------------------------------------------------------------------- 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 21 optimal weight: 3.9990 chunk 1 optimal weight: 0.0060 chunk 8 optimal weight: 0.2980 chunk 0 optimal weight: 0.1980 chunk 19 optimal weight: 8.9990 chunk 5 optimal weight: 0.0770 chunk 10 optimal weight: 0.4980 chunk 12 optimal weight: 0.0000 chunk 7 optimal weight: 0.1980 chunk 18 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 overall best weight: 0.0958 ------------------------------------------------------------------------------- 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 = 0.4934 r_free = 0.4934 target = 0.286026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.236912 restraints weight = 7901.989| |-----------------------------------------------------------------------------| r_work (start): 0.4524 rms_B_bonded: 2.39 r_work: 0.4342 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4257 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.3562 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= 0.123 Angle : 0.582 9.782 2947 Z= 0.311 Chirality : 0.037 0.128 321 Planarity : 0.003 0.027 373 Dihedral : 4.230 16.786 282 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.55), residues: 251 helix: 2.26 (0.46), residues: 130 sheet: 0.68 (0.95), residues: 34 loop : -1.32 (0.65), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 386 TYR 0.007 0.001 TYR f 600 PHE 0.014 0.002 PHE f 370 TRP 0.006 0.001 TRP f 542 HIS 0.002 0.001 HIS f 584 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 2199) covalent geometry : angle 0.58230 ( 2947) hydrogen bonds : bond 0.05979 ( 114) hydrogen bonds : angle 4.69188 ( 333) *********************** 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 44 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 0.8049 time to fit residues: 34.7759 Evaluate side-chains 40 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 400 THR Chi-restraints excluded: chain f residue 491 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 5 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 0.0970 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 9 optimal weight: 0.1980 overall best weight: 0.1778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 658 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.285333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.240184 restraints weight = 7813.785| |-----------------------------------------------------------------------------| r_work (start): 0.4510 rms_B_bonded: 2.72 r_work: 0.4258 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4176 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.4263 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= 0.153 Angle : 0.625 10.161 2947 Z= 0.326 Chirality : 0.038 0.126 321 Planarity : 0.004 0.031 373 Dihedral : 4.311 19.322 282 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.67 % Allowed : 12.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.54), residues: 251 helix: 2.37 (0.45), residues: 130 sheet: 0.37 (0.95), residues: 34 loop : -1.53 (0.62), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG f 361 TYR 0.009 0.002 TYR f 485 PHE 0.015 0.002 PHE f 370 TRP 0.005 0.001 TRP f 542 HIS 0.004 0.001 HIS f 687 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 2199) covalent geometry : angle 0.62453 ( 2947) hydrogen bonds : bond 0.06054 ( 114) hydrogen bonds : angle 4.58660 ( 333) *********************** 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 42 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 368 GLU cc_start: 0.5668 (OUTLIER) cc_final: 0.4485 (mm-30) outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.7286 time to fit residues: 30.7363 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 : 0.085 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 0.1980 chunk 2 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 0.0570 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.0670 chunk 24 optimal weight: 0.0970 overall best weight: 0.1034 ------------------------------------------------------------------------------- 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 = 0.4939 r_free = 0.4939 target = 0.285981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.238365 restraints weight = 7782.438| |-----------------------------------------------------------------------------| r_work (start): 0.4511 rms_B_bonded: 2.88 r_work: 0.4269 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4180 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.4608 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= 0.114 Angle : 0.565 9.878 2947 Z= 0.296 Chirality : 0.037 0.127 321 Planarity : 0.003 0.029 373 Dihedral : 4.139 17.865 282 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.26 % Allowed : 13.81 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.55), residues: 251 helix: 2.74 (0.45), residues: 131 sheet: 0.19 (0.95), residues: 34 loop : -1.56 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 361 TYR 0.007 0.001 TYR f 485 PHE 0.012 0.001 PHE f 370 TRP 0.005 0.001 TRP f 542 HIS 0.003 0.001 HIS f 584 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 2199) covalent geometry : angle 0.56474 ( 2947) hydrogen bonds : bond 0.05166 ( 114) hydrogen bonds : angle 4.43184 ( 333) *********************** 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 39 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.073 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 outliers start: 3 outliers final: 1 residues processed: 39 average time/residue: 0.7242 time to fit residues: 29.1309 Evaluate side-chains 36 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 400 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 0.1980 chunk 22 optimal weight: 0.2980 chunk 23 optimal weight: 0.1980 chunk 4 optimal weight: 0.0980 chunk 1 optimal weight: 0.0870 chunk 5 optimal weight: 0.0570 chunk 9 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 overall best weight: 0.1076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.286326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.240641 restraints weight = 7979.171| |-----------------------------------------------------------------------------| r_work (start): 0.4514 rms_B_bonded: 2.63 r_work: 0.4270 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4186 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.4818 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= 0.114 Angle : 0.562 9.849 2947 Z= 0.293 Chirality : 0.037 0.125 321 Planarity : 0.003 0.030 373 Dihedral : 4.050 16.778 282 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.09 % Allowed : 12.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.55), residues: 251 helix: 2.88 (0.45), residues: 131 sheet: -0.32 (0.91), residues: 40 loop : -1.49 (0.63), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 361 TYR 0.011 0.001 TYR f 597 PHE 0.011 0.001 PHE f 370 TRP 0.005 0.000 TRP f 542 HIS 0.002 0.001 HIS f 490 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 2199) covalent geometry : angle 0.56225 ( 2947) hydrogen bonds : bond 0.05005 ( 114) hydrogen bonds : angle 4.32870 ( 333) *********************** 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 41 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.080 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 491 GLU cc_start: 0.6091 (OUTLIER) cc_final: 0.5674 (tt0) outliers start: 5 outliers final: 2 residues processed: 41 average time/residue: 0.7105 time to fit residues: 29.9447 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 : 0.111 ------------------------------------------------------------------------------- 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 550 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 3 optimal weight: 0.0770 chunk 16 optimal weight: 7.9990 chunk 22 optimal weight: 0.0670 chunk 2 optimal weight: 0.0670 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 23 optimal weight: 0.3980 chunk 8 optimal weight: 0.3980 chunk 4 optimal weight: 0.0870 chunk 9 optimal weight: 0.1980 chunk 1 optimal weight: 0.0670 overall best weight: 0.0730 ------------------------------------------------------------------------------- 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 = 0.4937 r_free = 0.4937 target = 0.286654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.243217 restraints weight = 7912.625| |-----------------------------------------------------------------------------| r_work (start): 0.4551 rms_B_bonded: 2.79 r_work: 0.4305 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4221 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2199 Z= 0.105 Angle : 0.549 9.720 2947 Z= 0.286 Chirality : 0.037 0.125 321 Planarity : 0.003 0.027 373 Dihedral : 3.908 16.147 282 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.09 % Allowed : 12.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.57), residues: 251 helix: 3.24 (0.46), residues: 131 sheet: -0.33 (0.91), residues: 40 loop : -1.57 (0.63), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 361 TYR 0.013 0.001 TYR f 597 PHE 0.010 0.001 PHE f 370 TRP 0.005 0.001 TRP f 542 HIS 0.002 0.001 HIS f 396 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 2199) covalent geometry : angle 0.54871 ( 2947) hydrogen bonds : bond 0.04496 ( 114) hydrogen bonds : angle 4.21923 ( 333) *********************** 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 42 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 563 TYR cc_start: 0.5061 (m-10) cc_final: 0.4804 (m-10) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 0.7294 time to fit residues: 30.7806 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 : 0.115 ------------------------------------------------------------------------------- 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 432 ILE Chi-restraints excluded: chain f residue 550 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 4 optimal weight: 0.1980 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 chunk 7 optimal weight: 0.2980 chunk 9 optimal weight: 0.0770 chunk 6 optimal weight: 0.0770 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 10 optimal weight: 0.0870 chunk 24 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 overall best weight: 0.0872 ------------------------------------------------------------------------------- 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 = 0.4936 r_free = 0.4936 target = 0.286646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.241909 restraints weight = 7822.477| |-----------------------------------------------------------------------------| r_work (start): 0.4582 rms_B_bonded: 2.63 r_work: 0.4344 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4265 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2199 Z= 0.109 Angle : 0.575 9.857 2947 Z= 0.294 Chirality : 0.036 0.125 321 Planarity : 0.003 0.027 373 Dihedral : 3.906 15.782 282 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.67 % Allowed : 14.23 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.57), residues: 251 helix: 3.27 (0.46), residues: 131 sheet: -0.35 (0.90), residues: 40 loop : -1.61 (0.63), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 361 TYR 0.013 0.002 TYR f 597 PHE 0.010 0.001 PHE f 370 TRP 0.004 0.001 TRP f 542 HIS 0.001 0.001 HIS f 396 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 2199) covalent geometry : angle 0.57540 ( 2947) hydrogen bonds : bond 0.04558 ( 114) hydrogen bonds : angle 4.21921 ( 333) *********************** 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: 4 poor density : 34 time to evaluate : 0.085 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: 0.6747 (ttm170) cc_final: 0.3553 (ttt180) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.6847 time to fit residues: 26.0515 Evaluate side-chains 35 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 400 THR Chi-restraints excluded: chain f residue 432 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 0.0670 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.0870 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 0.0770 chunk 0 optimal weight: 0.1980 overall best weight: 0.1654 ------------------------------------------------------------------------------- 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 = 0.4928 r_free = 0.4928 target = 0.285550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.241257 restraints weight = 7860.098| |-----------------------------------------------------------------------------| r_work (start): 0.4509 rms_B_bonded: 2.72 r_work: 0.4262 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4172 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2199 Z= 0.141 Angle : 0.622 10.176 2947 Z= 0.319 Chirality : 0.037 0.125 321 Planarity : 0.004 0.045 373 Dihedral : 4.123 15.369 282 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.67 % Allowed : 13.81 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.56), residues: 251 helix: 3.04 (0.45), residues: 130 sheet: -0.39 (0.91), residues: 40 loop : -1.64 (0.62), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 361 TYR 0.011 0.002 TYR f 597 PHE 0.013 0.002 PHE f 620 TRP 0.004 0.001 TRP f 542 HIS 0.002 0.001 HIS f 490 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 2199) covalent geometry : angle 0.62155 ( 2947) hydrogen bonds : bond 0.05331 ( 114) hydrogen bonds : angle 4.29867 ( 333) *********************** 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 38 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.115 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: 0.6807 (ttm170) cc_final: 0.3602 (ttt180) REVERT: f 491 GLU cc_start: 0.6216 (OUTLIER) cc_final: 0.5811 (tt0) REVERT: f 597 TYR cc_start: 0.5719 (m-80) cc_final: 0.5457 (m-80) outliers start: 4 outliers final: 1 residues processed: 37 average time/residue: 0.7439 time to fit residues: 28.3396 Evaluate side-chains 36 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 400 THR Chi-restraints excluded: chain f residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 8 optimal weight: 0.3980 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 0.1980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.0770 chunk 5 optimal weight: 0.1980 chunk 24 optimal weight: 0.0570 overall best weight: 0.1856 ------------------------------------------------------------------------------- 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 = 0.4928 r_free = 0.4928 target = 0.285146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.243736 restraints weight = 7883.638| |-----------------------------------------------------------------------------| r_work (start): 0.4592 rms_B_bonded: 2.83 r_work: 0.4282 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4195 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2199 Z= 0.149 Angle : 0.625 10.157 2947 Z= 0.322 Chirality : 0.038 0.126 321 Planarity : 0.004 0.048 373 Dihedral : 4.209 15.203 282 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.26 % Allowed : 14.23 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.55), residues: 251 helix: 2.82 (0.45), residues: 131 sheet: -0.25 (0.93), residues: 40 loop : -1.87 (0.60), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 361 TYR 0.016 0.002 TYR f 626 PHE 0.014 0.002 PHE f 370 TRP 0.006 0.001 TRP f 542 HIS 0.003 0.001 HIS f 490 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 2199) covalent geometry : angle 0.62476 ( 2947) hydrogen bonds : bond 0.05623 ( 114) hydrogen bonds : angle 4.26874 ( 333) ********************** 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 36 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 361 ARG cc_start: 0.6859 (ttm170) cc_final: 0.5295 (ttt180) REVERT: f 597 TYR cc_start: 0.5628 (m-80) cc_final: 0.5285 (m-10) outliers start: 3 outliers final: 1 residues processed: 36 average time/residue: 0.7586 time to fit residues: 28.0998 Evaluate side-chains 34 residues out of total 239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 400 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 5 optimal weight: 0.1980 chunk 22 optimal weight: 0.0770 chunk 19 optimal weight: 8.9990 chunk 9 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 4 optimal weight: 0.0570 chunk 8 optimal weight: 0.2980 overall best weight: 0.1456 ------------------------------------------------------------------------------- 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 = 0.4929 r_free = 0.4929 target = 0.285550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.243899 restraints weight = 7885.769| |-----------------------------------------------------------------------------| r_work (start): 0.4532 rms_B_bonded: 2.86 r_work: 0.4223 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4134 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2199 Z= 0.130 Angle : 0.600 10.048 2947 Z= 0.312 Chirality : 0.037 0.126 321 Planarity : 0.004 0.037 373 Dihedral : 4.121 14.530 282 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.84 % Allowed : 15.06 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.56), residues: 251 helix: 2.85 (0.46), residues: 132 sheet: -0.18 (0.93), residues: 40 loop : -1.89 (0.62), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 361 TYR 0.012 0.002 TYR f 597 PHE 0.017 0.002 PHE f 620 TRP 0.005 0.001 TRP f 542 HIS 0.002 0.001 HIS f 396 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 2199) covalent geometry : angle 0.59960 ( 2947) hydrogen bonds : bond 0.05221 ( 114) hydrogen bonds : angle 4.20497 ( 333) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2843.10 seconds wall clock time: 48 minutes 45.19 seconds (2925.19 seconds total)