Starting phenix.real_space_refine on Thu Sep 10 22:45:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ok8_70556/09_2026/9ok8_70556.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ok8_70556/09_2026/9ok8_70556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ok8_70556/09_2026/9ok8_70556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ok8_70556/09_2026/9ok8_70556.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ok8_70556/09_2026/9ok8_70556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ok8_70556/09_2026/9ok8_70556.map" } resolution = 3.69 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= -0.001 sd= 0.032 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 P 3 5.49 5 S 32 5.16 5 C 2933 2.51 5 N 833 2.21 5 O 835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4636 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4605 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 583, 4600 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 27, 'TRANS': 555} Chain breaks: 14 Conformer: "B" Number of residues, atoms: 583, 4600 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 27, 'TRANS': 555} Chain breaks: 14 bond proxies already assigned to first conformer: 4668 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA A 826 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 826 " occ=0.50 Time building chain proxies: 1.80, per 1000 atoms: 0.39 Number of scatterers: 4636 At special positions: 0 Unit cell: (75.19, 67.89, 111.69, 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 32 16.00 P 3 15.00 O 835 8.00 N 833 7.00 C 2933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 395 " distance=2.04 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: 0.39 Conformation dependent library (CDL) restraints added in 296.2 milliseconds 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1092 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 47.9% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 180 through 186 removed outlier: 4.238A pdb=" N PHE A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 248 through 254 Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 365 through 377 Processing helix chain 'A' and resid 378 through 383 removed outlier: 4.396A pdb=" N PHE A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 404 removed outlier: 3.835A pdb=" N CYS A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 396 " --> pdb=" O TRP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 removed outlier: 3.791A pdb=" N VAL A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 461 through 467 removed outlier: 3.841A pdb=" N LEU A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 480 removed outlier: 3.684A pdb=" N THR A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 511 removed outlier: 4.259A pdb=" N GLN A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 516 Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.632A pdb=" N GLY A 532 " --> pdb=" O THR A 528 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 556 through 563 Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'A' and resid 616 through 627 Processing helix chain 'A' and resid 630 through 639 removed outlier: 3.540A pdb=" N VAL A 634 " --> pdb=" O GLU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 665 Processing helix chain 'A' and resid 744 through 753 Processing helix chain 'A' and resid 772 through 781 removed outlier: 4.121A pdb=" N LEU A 776 " --> pdb=" O GLY A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 809 removed outlier: 4.062A pdb=" N TYR A 803 " --> pdb=" O ARG A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 839 removed outlier: 4.210A pdb=" N THR A 830 " --> pdb=" O AALA A 826 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLN A 839 " --> pdb=" O VAL A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 868 Processing sheet with id=AA1, first strand: chain 'A' and resid 671 through 674 Processing sheet with id=AA2, first strand: chain 'A' and resid 845 through 846 removed outlier: 3.765A pdb=" N LEU A 846 " --> pdb=" O VAL A 872 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 165 hydrogen bonds defined for protein. 477 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: 0.51 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1542 1.35 - 1.49: 1072 1.49 - 1.62: 2058 1.62 - 1.75: 0 1.75 - 1.89: 41 Bond restraints: 4713 Sorted by residual: bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.17e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.79e+01 bond pdb=" C8 ATP A 901 " pdb=" N7 ATP A 901 " ideal model delta sigma weight residual 1.310 1.354 -0.044 1.00e-02 1.00e+04 1.92e+01 bond pdb=" C4 ATP A 901 " pdb=" N9 ATP A 901 " ideal model delta sigma weight residual 1.374 1.330 0.044 1.00e-02 1.00e+04 1.90e+01 bond pdb=" C5 ATP A 901 " pdb=" N7 ATP A 901 " ideal model delta sigma weight residual 1.387 1.346 0.041 1.00e-02 1.00e+04 1.72e+01 ... (remaining 4708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 6284 3.87 - 7.74: 67 7.74 - 11.61: 5 11.61 - 15.48: 0 15.48 - 19.35: 2 Bond angle restraints: 6358 Sorted by residual: angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 120.52 19.35 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PA ATP A 901 " pdb=" O3A ATP A 901 " pdb=" PB ATP A 901 " ideal model delta sigma weight residual 136.83 119.95 16.88 1.00e+00 1.00e+00 2.85e+02 angle pdb=" C5 ATP A 901 " pdb=" C4 ATP A 901 " pdb=" N3 ATP A 901 " ideal model delta sigma weight residual 126.80 118.70 8.10 1.00e+00 1.00e+00 6.57e+01 angle pdb=" N3 ATP A 901 " pdb=" C4 ATP A 901 " pdb=" N9 ATP A 901 " ideal model delta sigma weight residual 127.04 135.06 -8.02 1.15e+00 7.59e-01 4.88e+01 angle pdb=" N GLY A 549 " pdb=" CA GLY A 549 " pdb=" C GLY A 549 " ideal model delta sigma weight residual 115.59 106.63 8.96 1.32e+00 5.74e-01 4.61e+01 ... (remaining 6353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 2531 16.56 - 33.13: 283 33.13 - 49.69: 47 49.69 - 66.25: 23 66.25 - 82.82: 7 Dihedral angle restraints: 2891 sinusoidal: 1213 harmonic: 1678 Sorted by residual: dihedral pdb=" CA ALA A 722 " pdb=" C ALA A 722 " pdb=" N MET A 723 " pdb=" CA MET A 723 " ideal model delta harmonic sigma weight residual 180.00 149.13 30.87 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA GLN A 535 " pdb=" C GLN A 535 " pdb=" N PRO A 536 " pdb=" CA PRO A 536 " ideal model delta harmonic sigma weight residual 180.00 152.51 27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA VAL A 432 " pdb=" C VAL A 432 " pdb=" N ALA A 433 " pdb=" CA ALA A 433 " ideal model delta harmonic sigma weight residual -180.00 -158.12 -21.88 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 2888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 575 0.058 - 0.117: 129 0.117 - 0.175: 16 0.175 - 0.233: 2 0.233 - 0.292: 1 Chirality restraints: 723 Sorted by residual: chirality pdb=" CG LEU A 550 " pdb=" CB LEU A 550 " pdb=" CD1 LEU A 550 " pdb=" CD2 LEU A 550 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CG LEU A 773 " pdb=" CB LEU A 773 " pdb=" CD1 LEU A 773 " pdb=" CD2 LEU A 773 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" CB VAL A 744 " pdb=" CA VAL A 744 " pdb=" CG1 VAL A 744 " pdb=" CG2 VAL A 744 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 720 not shown) Planarity restraints: 809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 347 " 0.587 9.50e-02 1.11e+02 2.63e-01 4.23e+01 pdb=" NE ARG A 347 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 347 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 347 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 347 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 438 " -0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C LEU A 438 " 0.057 2.00e-02 2.50e+03 pdb=" O LEU A 438 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 439 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 654 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C MET A 654 " -0.050 2.00e-02 2.50e+03 pdb=" O MET A 654 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP A 655 " 0.017 2.00e-02 2.50e+03 ... (remaining 806 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 182 2.69 - 3.24: 5133 3.24 - 3.79: 7674 3.79 - 4.35: 10222 4.35 - 4.90: 15298 Nonbonded interactions: 38509 Sorted by model distance: nonbonded pdb=" O ARG A 746 " pdb=" OG SER A 749 " model vdw 2.132 3.040 nonbonded pdb=" ND2 ASN A 378 " pdb=" OG1 THR A 380 " model vdw 2.170 3.120 nonbonded pdb=" OE1 GLN A 582 " pdb=" OH TYR A 617 " model vdw 2.177 3.040 nonbonded pdb=" NH1 ARG A 447 " pdb=" OE1 GLU A 514 " model vdw 2.234 3.120 nonbonded pdb=" OE2 GLU A 760 " pdb=" NH1 ARG A 791 " model vdw 2.242 3.120 ... (remaining 38504 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.370 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.640 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 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 : 0.005 0.081 4714 Z= 0.356 Angle : 1.044 19.350 6360 Z= 0.681 Chirality : 0.051 0.292 723 Planarity : 0.012 0.263 809 Dihedral : 15.201 82.815 1796 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 28.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.74 % Favored : 86.26 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 are not related in a simple way. whole: -3.86 (0.32), residues: 556 helix: -1.47 (0.31), residues: 239 sheet: -3.49 (0.88), residues: 28 loop : -3.55 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 799 TYR 0.012 0.002 TYR A 803 PHE 0.029 0.003 PHE A 422 TRP 0.027 0.003 TRP A 578 HIS 0.012 0.001 HIS A 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.36 ( 4713) covalent geometry : angle 1.03288 / 0.68 ( 6358) SS BOND : bond 0.00576 / 0.30 ( 1) SS BOND : angle 8.78155 / 4.69 ( 2) hydrogen bonds : bond 0.15449 / 11.04 ( 165) hydrogen bonds : angle 7.06186 / 5.04 ( 477) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 715 LEU cc_start: 0.7723 (mt) cc_final: 0.7410 (tt) REVERT: A 799 ARG cc_start: 0.5562 (tpt170) cc_final: 0.5339 (tpt90) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1013 time to fit residues: 11.4390 Evaluate side-chains 66 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.191002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.162957 restraints weight = 8798.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.168453 restraints weight = 5389.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.172141 restraints weight = 3748.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.174693 restraints weight = 2858.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.176518 restraints weight = 2323.726| |-----------------------------------------------------------------------------| r_work (final): 0.4644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4644 r_free = 0.4644 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4644 r_free = 0.4644 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4714 Z= 0.170 Angle : 0.858 11.454 6360 Z= 0.433 Chirality : 0.047 0.287 723 Planarity : 0.007 0.068 809 Dihedral : 8.313 86.138 671 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 24.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 2.02 % Allowed : 10.30 % Favored : 87.68 % 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 are not related in a simple way. whole: -3.67 (0.31), residues: 556 helix: -1.19 (0.31), residues: 230 sheet: -3.94 (0.87), residues: 27 loop : -3.45 (0.30), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 447 TYR 0.016 0.002 TYR A 357 PHE 0.017 0.002 PHE A 231 TRP 0.009 0.001 TRP A 578 HIS 0.016 0.002 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 4713) covalent geometry : angle 0.85208 / 0.43 ( 6358) SS BOND : bond 0.00752 / 0.40 ( 1) SS BOND : angle 5.56657 / 3.05 ( 2) hydrogen bonds : bond 0.05304 / 3.47 ( 165) hydrogen bonds : angle 6.07308 / 4.22 ( 477) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.6896 (ppp) cc_final: 0.6680 (ppp) REVERT: A 378 ASN cc_start: 0.6670 (OUTLIER) cc_final: 0.6214 (p0) REVERT: A 556 MET cc_start: 0.5115 (OUTLIER) cc_final: 0.4676 (tpt) REVERT: A 715 LEU cc_start: 0.7778 (mt) cc_final: 0.7367 (tt) outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 0.0885 time to fit residues: 10.1556 Evaluate side-chains 75 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 853 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.193198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.165326 restraints weight = 9078.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.170820 restraints weight = 5539.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.174435 restraints weight = 3875.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.176935 restraints weight = 2972.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.178436 restraints weight = 2433.907| |-----------------------------------------------------------------------------| r_work (final): 0.4666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4666 r_free = 0.4666 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4666 r_free = 0.4666 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4714 Z= 0.159 Angle : 0.832 10.158 6360 Z= 0.417 Chirality : 0.045 0.157 723 Planarity : 0.007 0.072 809 Dihedral : 8.300 81.907 671 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 24.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 2.83 % Allowed : 15.35 % Favored : 81.82 % 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 are not related in a simple way. whole: -3.33 (0.32), residues: 556 helix: -0.87 (0.32), residues: 230 sheet: -3.77 (0.87), residues: 27 loop : -3.30 (0.31), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 447 TYR 0.016 0.001 TYR A 617 PHE 0.016 0.002 PHE A 231 TRP 0.011 0.001 TRP A 578 HIS 0.006 0.001 HIS A 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 4713) covalent geometry : angle 0.82791 / 0.42 ( 6358) SS BOND : bond 0.00865 / 0.46 ( 1) SS BOND : angle 4.94368 / 2.77 ( 2) hydrogen bonds : bond 0.04952 / 3.19 ( 165) hydrogen bonds : angle 5.85292 / 4.04 ( 477) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ASN cc_start: 0.6280 (OUTLIER) cc_final: 0.5974 (p0) REVERT: A 556 MET cc_start: 0.4843 (OUTLIER) cc_final: 0.4485 (tpt) outliers start: 14 outliers final: 10 residues processed: 83 average time/residue: 0.0880 time to fit residues: 9.0743 Evaluate side-chains 79 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 790 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 49 optimal weight: 0.0270 chunk 37 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 GLN A 856 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.197646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.170401 restraints weight = 9385.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.176166 restraints weight = 5438.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.179892 restraints weight = 3715.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.182484 restraints weight = 2831.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.184009 restraints weight = 2302.620| |-----------------------------------------------------------------------------| r_work (final): 0.4710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4710 r_free = 0.4710 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4710 r_free = 0.4710 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4714 Z= 0.150 Angle : 0.810 9.914 6360 Z= 0.402 Chirality : 0.044 0.176 723 Planarity : 0.007 0.075 809 Dihedral : 8.199 80.824 671 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 23.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 3.64 % Allowed : 17.98 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.33), residues: 556 helix: -0.69 (0.33), residues: 232 sheet: -3.99 (0.79), residues: 31 loop : -3.18 (0.31), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 799 TYR 0.015 0.001 TYR A 803 PHE 0.015 0.002 PHE A 231 TRP 0.009 0.001 TRP A 578 HIS 0.005 0.001 HIS A 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 4713) covalent geometry : angle 0.80583 / 0.40 ( 6358) SS BOND : bond 0.00892 / 0.47 ( 1) SS BOND : angle 4.82962 / 2.73 ( 2) hydrogen bonds : bond 0.04899 / 3.13 ( 165) hydrogen bonds : angle 5.75390 / 3.99 ( 477) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ASN cc_start: 0.5672 (OUTLIER) cc_final: 0.4581 (p0) REVERT: A 737 HIS cc_start: 0.5693 (p-80) cc_final: 0.5470 (p90) REVERT: A 799 ARG cc_start: 0.5841 (tpt170) cc_final: 0.5486 (tpt90) outliers start: 18 outliers final: 13 residues processed: 80 average time/residue: 0.0846 time to fit residues: 8.4386 Evaluate side-chains 85 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 723 MET Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 794 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 0.0970 chunk 13 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 GLN ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.198234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.171484 restraints weight = 9305.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.177272 restraints weight = 5411.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.181043 restraints weight = 3702.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.183618 restraints weight = 2803.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.185200 restraints weight = 2269.708| |-----------------------------------------------------------------------------| r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4718 r_free = 0.4718 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4718 r_free = 0.4718 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4714 Z= 0.152 Angle : 0.803 9.761 6360 Z= 0.398 Chirality : 0.044 0.174 723 Planarity : 0.006 0.075 809 Dihedral : 8.179 80.476 671 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 3.43 % Allowed : 19.39 % Favored : 77.17 % 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 are not related in a simple way. whole: -3.17 (0.33), residues: 556 helix: -0.84 (0.32), residues: 241 sheet: -3.84 (0.84), residues: 31 loop : -3.13 (0.32), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 664 TYR 0.013 0.001 TYR A 803 PHE 0.014 0.002 PHE A 231 TRP 0.009 0.001 TRP A 578 HIS 0.004 0.001 HIS A 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 4713) covalent geometry : angle 0.79856 / 0.40 ( 6358) SS BOND : bond 0.00891 / 0.47 ( 1) SS BOND : angle 4.86893 / 2.76 ( 2) hydrogen bonds : bond 0.04807 / 3.09 ( 165) hydrogen bonds : angle 5.63630 / 3.92 ( 477) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 GLN cc_start: 0.8983 (mp-120) cc_final: 0.8732 (mt0) REVERT: A 378 ASN cc_start: 0.5644 (OUTLIER) cc_final: 0.5410 (p0) REVERT: A 737 HIS cc_start: 0.5669 (p-80) cc_final: 0.5467 (p90) REVERT: A 799 ARG cc_start: 0.5884 (tpt170) cc_final: 0.5601 (tpt90) outliers start: 17 outliers final: 13 residues processed: 82 average time/residue: 0.0801 time to fit residues: 8.3083 Evaluate side-chains 83 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 723 MET Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 790 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 0.1980 chunk 39 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 GLN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.200538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.174266 restraints weight = 9483.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.180004 restraints weight = 5563.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.183768 restraints weight = 3779.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.186337 restraints weight = 2866.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.187994 restraints weight = 2305.096| |-----------------------------------------------------------------------------| r_work (final): 0.4756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4754 r_free = 0.4754 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4754 r_free = 0.4754 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4714 Z= 0.141 Angle : 0.801 12.450 6360 Z= 0.393 Chirality : 0.043 0.167 723 Planarity : 0.007 0.080 809 Dihedral : 8.077 80.260 671 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 3.23 % Allowed : 19.60 % Favored : 77.17 % 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 are not related in a simple way. whole: -3.16 (0.33), residues: 556 helix: -0.80 (0.32), residues: 247 sheet: -3.81 (0.83), residues: 31 loop : -3.22 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 664 TYR 0.013 0.001 TYR A 803 PHE 0.016 0.002 PHE A 422 TRP 0.007 0.001 TRP A 578 HIS 0.004 0.001 HIS A 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 4713) covalent geometry : angle 0.79709 / 0.39 ( 6358) SS BOND : bond 0.00818 / 0.43 ( 1) SS BOND : angle 4.59051 / 2.60 ( 2) hydrogen bonds : bond 0.04550 / 2.93 ( 165) hydrogen bonds : angle 5.47529 / 3.83 ( 477) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 ASN cc_start: 0.5518 (OUTLIER) cc_final: 0.5275 (p0) outliers start: 16 outliers final: 14 residues processed: 84 average time/residue: 0.0778 time to fit residues: 8.1809 Evaluate side-chains 83 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 723 MET Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 858 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 chunk 29 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN A 378 ASN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.196598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.168797 restraints weight = 9378.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.174370 restraints weight = 5705.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.178326 restraints weight = 3970.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.181110 restraints weight = 3003.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.182930 restraints weight = 2414.286| |-----------------------------------------------------------------------------| r_work (final): 0.4706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4706 r_free = 0.4706 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4706 r_free = 0.4706 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5866 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4714 Z= 0.141 Angle : 0.806 11.281 6360 Z= 0.395 Chirality : 0.043 0.150 723 Planarity : 0.006 0.079 809 Dihedral : 8.031 79.814 671 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 3.64 % Allowed : 19.80 % Favored : 76.57 % 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 are not related in a simple way. whole: -3.10 (0.33), residues: 556 helix: -0.77 (0.32), residues: 247 sheet: -3.78 (0.82), residues: 31 loop : -3.16 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 664 TYR 0.015 0.001 TYR A 357 PHE 0.027 0.002 PHE A 422 TRP 0.008 0.001 TRP A 578 HIS 0.004 0.001 HIS A 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 4713) covalent geometry : angle 0.80225 / 0.39 ( 6358) SS BOND : bond 0.00910 / 0.48 ( 1) SS BOND : angle 4.54980 / 2.59 ( 2) hydrogen bonds : bond 0.04515 / 2.89 ( 165) hydrogen bonds : angle 5.48141 / 3.83 ( 477) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ASN cc_start: 0.5469 (OUTLIER) cc_final: 0.5206 (p0) REVERT: A 451 GLU cc_start: 0.5268 (OUTLIER) cc_final: 0.5001 (tt0) outliers start: 18 outliers final: 13 residues processed: 82 average time/residue: 0.0749 time to fit residues: 7.7692 Evaluate side-chains 81 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 790 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 55 optimal weight: 0.0970 chunk 43 optimal weight: 0.0870 chunk 52 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN A 476 GLN A 573 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.197581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.169590 restraints weight = 9464.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.175445 restraints weight = 5646.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.179584 restraints weight = 3852.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.182432 restraints weight = 2866.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.184114 restraints weight = 2288.407| |-----------------------------------------------------------------------------| r_work (final): 0.4722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4722 r_free = 0.4722 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4722 r_free = 0.4722 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4714 Z= 0.143 Angle : 0.838 10.773 6360 Z= 0.408 Chirality : 0.043 0.150 723 Planarity : 0.006 0.073 809 Dihedral : 8.007 79.635 671 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 3.64 % Allowed : 19.80 % Favored : 76.57 % 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 are not related in a simple way. whole: -3.02 (0.33), residues: 556 helix: -0.74 (0.32), residues: 247 sheet: -3.77 (0.80), residues: 31 loop : -3.07 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 799 TYR 0.013 0.001 TYR A 357 PHE 0.025 0.002 PHE A 422 TRP 0.007 0.001 TRP A 578 HIS 0.004 0.001 HIS A 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 4713) covalent geometry : angle 0.83440 / 0.41 ( 6358) SS BOND : bond 0.00876 / 0.46 ( 1) SS BOND : angle 4.47135 / 2.54 ( 2) hydrogen bonds : bond 0.04456 / 2.84 ( 165) hydrogen bonds : angle 5.36800 / 3.75 ( 477) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 GLU cc_start: 0.5260 (OUTLIER) cc_final: 0.4982 (tt0) REVERT: A 572 LYS cc_start: 0.6551 (mmmt) cc_final: 0.5872 (mttm) outliers start: 18 outliers final: 15 residues processed: 80 average time/residue: 0.0825 time to fit residues: 8.2139 Evaluate side-chains 81 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 858 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 51 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 0.0470 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.198370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.170810 restraints weight = 9338.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.176568 restraints weight = 5604.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.180509 restraints weight = 3866.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.183246 restraints weight = 2908.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.184657 restraints weight = 2334.115| |-----------------------------------------------------------------------------| r_work (final): 0.4723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4722 r_free = 0.4722 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4722 r_free = 0.4722 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5856 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4714 Z= 0.142 Angle : 0.832 10.398 6360 Z= 0.405 Chirality : 0.043 0.150 723 Planarity : 0.006 0.071 809 Dihedral : 7.964 78.986 671 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 3.23 % Allowed : 19.80 % Favored : 76.97 % 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 are not related in a simple way. whole: -2.96 (0.33), residues: 556 helix: -0.74 (0.32), residues: 249 sheet: -3.72 (0.80), residues: 31 loop : -3.00 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 799 TYR 0.014 0.001 TYR A 357 PHE 0.023 0.002 PHE A 422 TRP 0.007 0.001 TRP A 578 HIS 0.003 0.001 HIS A 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 4713) covalent geometry : angle 0.82812 / 0.40 ( 6358) SS BOND : bond 0.00848 / 0.45 ( 1) SS BOND : angle 4.49395 / 2.55 ( 2) hydrogen bonds : bond 0.04472 / 2.86 ( 165) hydrogen bonds : angle 5.29749 / 3.69 ( 477) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 GLU cc_start: 0.5253 (OUTLIER) cc_final: 0.4977 (tt0) REVERT: A 556 MET cc_start: 0.5882 (tpt) cc_final: 0.5162 (ptm) REVERT: A 572 LYS cc_start: 0.6495 (mmmt) cc_final: 0.5941 (mttm) outliers start: 16 outliers final: 14 residues processed: 81 average time/residue: 0.0849 time to fit residues: 8.5610 Evaluate side-chains 83 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 790 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 49 optimal weight: 0.2980 chunk 5 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.194671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.165494 restraints weight = 9336.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.171383 restraints weight = 5569.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.175416 restraints weight = 3850.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.178364 restraints weight = 2903.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.180311 restraints weight = 2321.839| |-----------------------------------------------------------------------------| r_work (final): 0.4675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4675 r_free = 0.4675 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4675 r_free = 0.4675 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 4714 Z= 0.163 Angle : 0.878 16.306 6360 Z= 0.423 Chirality : 0.044 0.156 723 Planarity : 0.007 0.081 809 Dihedral : 8.045 79.060 671 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 3.23 % Allowed : 20.61 % Favored : 76.16 % 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 are not related in a simple way. whole: -3.00 (0.33), residues: 556 helix: -0.78 (0.32), residues: 248 sheet: -3.72 (0.81), residues: 31 loop : -3.02 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 123 TYR 0.018 0.002 TYR A 357 PHE 0.020 0.002 PHE A 422 TRP 0.008 0.002 TRP A 392 HIS 0.003 0.001 HIS A 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 4713) covalent geometry : angle 0.87396 / 0.42 ( 6358) SS BOND : bond 0.00888 / 0.47 ( 1) SS BOND : angle 4.89322 / 2.78 ( 2) hydrogen bonds : bond 0.04684 / 3.02 ( 165) hydrogen bonds : angle 5.41989 / 3.76 ( 477) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1112 Ramachandran restraints generated. 556 Oldfield, 0 Emsley, 556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 GLU cc_start: 0.5302 (OUTLIER) cc_final: 0.4986 (tt0) REVERT: A 572 LYS cc_start: 0.6606 (mmmt) cc_final: 0.6038 (mttm) REVERT: A 799 ARG cc_start: 0.6071 (tpt90) cc_final: 0.5867 (tpt90) outliers start: 16 outliers final: 15 residues processed: 80 average time/residue: 0.0833 time to fit residues: 8.3581 Evaluate side-chains 82 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 562 HIS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 858 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 0.0010 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 GLN ** A 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.197777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.169312 restraints weight = 9367.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.175278 restraints weight = 5550.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.179414 restraints weight = 3796.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.182371 restraints weight = 2842.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.184370 restraints weight = 2249.102| |-----------------------------------------------------------------------------| r_work (final): 0.4722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4719 r_free = 0.4719 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4719 r_free = 0.4719 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4714 Z= 0.145 Angle : 0.877 15.134 6360 Z= 0.419 Chirality : 0.044 0.152 723 Planarity : 0.007 0.077 809 Dihedral : 7.975 80.174 671 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 3.23 % Allowed : 21.21 % Favored : 75.56 % 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 are not related in a simple way. whole: -2.90 (0.33), residues: 556 helix: -0.71 (0.32), residues: 250 sheet: -3.68 (0.80), residues: 31 loop : -2.96 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 123 TYR 0.013 0.001 TYR A 357 PHE 0.029 0.002 PHE A 422 TRP 0.006 0.001 TRP A 578 HIS 0.004 0.001 HIS A 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 4713) covalent geometry : angle 0.87347 / 0.42 ( 6358) SS BOND : bond 0.00803 / 0.42 ( 1) SS BOND : angle 4.53843 / 2.58 ( 2) hydrogen bonds : bond 0.04479 / 2.85 ( 165) hydrogen bonds : angle 5.38471 / 3.75 ( 477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1217.03 seconds wall clock time: 21 minutes 39.06 seconds (1299.06 seconds total)